Ug-E.coli rMAP Comprehensive Analysis Report Summary

This run was generated using rMAP version performed on 2021-09-03… Thank you for using this pipeline!!

Quick links

• Assembly summary statistics

• SNP-Variant Calling

• Phylogenetic inference

• Antimicrobial Resistance Profiling

• Plasmid Profiling

• Virulence Factor Determination

• Multi-Locus Sequence Typing (MLST)

• Pangenome Analysis

• Insertion sequence characterization (IS)

• Citations and Bibliography

Assembly summary statistics

Field	Description
SampleID	Name of the sample
TrimReads	Total number of reads after quality filtering
MeanReadLen	Average read length after quality filtering
Contigs	Number of contigs of the draft genome (>200bp)
GenomeLength	Length (bp) of the draft genome
LargestContig	Length (bp) of the largest contig in the genome
N50	Length of the smallest contig in the set that contains the fewest (largest) contigs whose combined length represents at least 50% of the assembly
GC-Content	GC content (%) of the draft genome
Depth	Number of times each nucleotide position in the draft genome has a read that aligns to that position

SampleID	TrimReads	MeanReadLen	Contigs	GenomeLength	LargestContig	N50	GC-Content	Depth
ID005zero	447672	129	70	4993383	556160	211386	50.60	11X
ID008	146	143	45	14384	415	358	50.15	1X
ID009	445827	137	647	5264283	116466	16469	57.36	11X
ID011	419430	133	323	5149794	151142	60552	50.75	10X
ID013	419323	132	2235	5680236	50661	4337	50.83	9X
ID014at24	402967	131	3801	7480294	39874	2836	50.64	7X
ID015HW	417149	132	127	4946518	258577	101369	50.83	11X
ID015at48	348445	134	141	4946083	261874	77897	50.83	9X
ID016at24	376407	134	164	5066617	206105	69000	50.76	9X
ID017at48	265213	137	281	5060662	148849	43286	50.71	7X
ID018at24	332021	133	112	5053728	322917	114340	50.53	8X
ID020at24	321023	133	150	4694658	304850	83486	50.63	9X
ID021at24	437154	132	149	4781760	208787	59208	50.64	12X
ID025III	47954	138	5432	5396283	7641	1066	53.02	1X
ID025II	409299	134	165	5064739	234487	77657	50.76	10X
ID025I	361054	132	133	5074111	342735	98841	50.77	9X
ID026	306128	128	133	5093392	293921	97680	50.72	7X
ID027	457381	129	151	5083310	252391	97639	50.74	11X
ID031	424851	132	91	5277895	439752	172240	50.57	10X
ID032I	371633	130	89	5249727	330993	158921	50.66	9X
ID033I	419857	129	131	4526608	244172	79601	50.73	11X
ID034II	407964	131	131	5072404	280895	106187	50.77	10X
ID034I	508184	133	141	5081530	254507	97496	50.74	13X
ID037	337693	132	149	4757913	225519	61221	50.78	9X
ID043I	377261	133	114	5131371	345412	117539	50.59	9X
ID045	319002	132	112	5080013	283826	147986	50.64	8X
ID047	335646	130	150	5226487	452233	102284	50.63	8X
ID050	531211	130	118	4897826	311054	106189	50.72	14X
ID051	311902	133	4256	6328658	38558	1853	50.21	6X
ID052	414620	132	171	5411328	295749	85770	50.48	10X
ID057	76108	134	142	4831648	201994	67497	50.64	2X
ID058	310873	132	2480	5006051	48769	2892	50.48	8X
ID066	457516	130	113	5009011	371379	179450	50.90	11X
ID070	401224	130	153	4932282	417517	83079	50.78	10X
ID073	380771	133	210	4913690	229261	59510	50.76	10X
ID081	352398	132	141	4937691	306082	83508	50.67	9X
ID096I	344533	137	358	5445707	100747	32529	57.15	8X
ID098	317029	133	721	5685500	149812	33837	50.40	7X
ID099	434039	133	136	4655534	221218	88674	50.72	12X
ID24	322189	130	115	5086874	314853	125472	50.76	8X

Select the parameter

Number of reads

Average number of reads per sample = 359277

Average read length

Average read length per sample = 133 bp

Number of contigs

Average number of contigs per sample = 612

Genome length

Average genome length per sample = 5034750 bp

Largest contig length

Average largest contig length per sample = 240554 bp

N50

Average N50 per sample = 80279 bp

GC content

Average GC content per sample = 51.051%

Sequencing depth

Average sequencing depth = 8.85X

Back to index

SNP-variant calling

Field	Description
GenomePosition	Position in the genome where SNP is found
Type	Nature of the SNP identified (Only ‘True’ SNPs are shown by default)
ReferenceAllele	Allele found in the reference genome
AlternateAllele	Allele found in the genome of interest forming the SNP
Consequence	Amino acid alterations caused by the SNP
AffectedGene	The tartget gene affected by the SNP
Product	The outcome from the presence of the SNP

Select the sample

ID005zero

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318124	snp	A	G	missense_variant c.196T>C p.Tyr66His	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
743316	snp	G	C	missense_variant c.490G>C p.Val164Leu	ybgI	radiation resistance protein YbgI
1006557	snp	C	T	missense_variant c.1044G>A p.Met348Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441532	snp	C	T	missense_variant c.212G>A p.Ser71Asn	hslJ	lipoprotein implicated in Novobiocin resistance
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227353	snp	A	G	missense_variant c.1406T>C p.Leu469Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227422	snp	G	C	missense_variant c.1337C>G p.Pro446Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227443	snp	G	C	missense_variant c.1316C>G p.Ala439Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227476	snp	C	G	missense_variant c.1283G>C p.Arg428Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227641	snp	T	A	missense_variant c.1118A>T p.Gln373Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227767	snp	G	A	missense_variant c.992C>T p.Ser331Phe	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227872	snp	G	C	missense_variant c.887C>G p.Pro296Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227968	snp	A	G	missense_variant c.791T>C p.Leu264Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228004	snp	C	A	missense_variant c.755G>T p.Gly252Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228444	snp	T	G	missense_variant c.315A>C p.Arg105Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228567	snp	T	C	missense_variant c.192A>G p.Ile64Met	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228649	snp	G	A	missense_variant c.110C>T p.Pro37Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228654	snp	T	G	missense_variant c.105A>C p.Gln35His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630612	snp	A	G	missense_variant c.287A>G p.Lys96Arg	yfgI	nalidixic acid resistance protein YfgI
3635776	snp	G	T	missense_variant c.936G>T p.Met312Ile	yhiM	inner membrane protein with a role in acid resistance
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
3870310	snp	T	A	missense_variant c.934T>A p.Trp312Arg	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103326	snp	G	A	missense_variant c.505G>A p.Val169Met	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID008

## Error in read.table("ID008_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318124	snp	A	G	missense_variant c.196T>C p.Tyr66His	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
743316	snp	G	C	missense_variant c.490G>C p.Val164Leu	ybgI	radiation resistance protein YbgI
1006557	snp	C	T	missense_variant c.1044G>A p.Met348Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441532	snp	C	T	missense_variant c.212G>A p.Ser71Asn	hslJ	lipoprotein implicated in Novobiocin resistance
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227353	snp	A	G	missense_variant c.1406T>C p.Leu469Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227422	snp	G	C	missense_variant c.1337C>G p.Pro446Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227443	snp	G	C	missense_variant c.1316C>G p.Ala439Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227476	snp	C	G	missense_variant c.1283G>C p.Arg428Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227641	snp	T	A	missense_variant c.1118A>T p.Gln373Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227767	snp	G	A	missense_variant c.992C>T p.Ser331Phe	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227872	snp	G	C	missense_variant c.887C>G p.Pro296Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227968	snp	A	G	missense_variant c.791T>C p.Leu264Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228004	snp	C	A	missense_variant c.755G>T p.Gly252Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228444	snp	T	G	missense_variant c.315A>C p.Arg105Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228567	snp	T	C	missense_variant c.192A>G p.Ile64Met	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228649	snp	G	A	missense_variant c.110C>T p.Pro37Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228654	snp	T	G	missense_variant c.105A>C p.Gln35His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630612	snp	A	G	missense_variant c.287A>G p.Lys96Arg	yfgI	nalidixic acid resistance protein YfgI
3635776	snp	G	T	missense_variant c.936G>T p.Met312Ile	yhiM	inner membrane protein with a role in acid resistance
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
3870310	snp	T	A	missense_variant c.934T>A p.Trp312Arg	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103326	snp	G	A	missense_variant c.505G>A p.Val169Met	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID009

## Error in read.table("ID009_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318124	snp	A	G	missense_variant c.196T>C p.Tyr66His	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
743316	snp	G	C	missense_variant c.490G>C p.Val164Leu	ybgI	radiation resistance protein YbgI
1006557	snp	C	T	missense_variant c.1044G>A p.Met348Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441532	snp	C	T	missense_variant c.212G>A p.Ser71Asn	hslJ	lipoprotein implicated in Novobiocin resistance
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227353	snp	A	G	missense_variant c.1406T>C p.Leu469Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227422	snp	G	C	missense_variant c.1337C>G p.Pro446Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227443	snp	G	C	missense_variant c.1316C>G p.Ala439Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227476	snp	C	G	missense_variant c.1283G>C p.Arg428Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227641	snp	T	A	missense_variant c.1118A>T p.Gln373Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227767	snp	G	A	missense_variant c.992C>T p.Ser331Phe	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227872	snp	G	C	missense_variant c.887C>G p.Pro296Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227968	snp	A	G	missense_variant c.791T>C p.Leu264Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228004	snp	C	A	missense_variant c.755G>T p.Gly252Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228444	snp	T	G	missense_variant c.315A>C p.Arg105Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228567	snp	T	C	missense_variant c.192A>G p.Ile64Met	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228649	snp	G	A	missense_variant c.110C>T p.Pro37Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228654	snp	T	G	missense_variant c.105A>C p.Gln35His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630612	snp	A	G	missense_variant c.287A>G p.Lys96Arg	yfgI	nalidixic acid resistance protein YfgI
3635776	snp	G	T	missense_variant c.936G>T p.Met312Ile	yhiM	inner membrane protein with a role in acid resistance
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
3870310	snp	T	A	missense_variant c.934T>A p.Trp312Arg	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103326	snp	G	A	missense_variant c.505G>A p.Val169Met	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID011

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1441517	snp	A	T	missense_variant c.227T>A p.Leu76Gln	hslJ	lipoprotein implicated in Novobiocin resistance
1441697	snp	C	T	missense_variant c.47G>A p.Gly16Glu	hslJ	lipoprotein implicated in Novobiocin resistance
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID013

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID014at24

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4103456	snp	G	A	missense_variant c.635G>A p.Gly212Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID015HW

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1006886	snp	C	T	missense_variant c.715G>A p.Gly239Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007267	snp	C	T	missense_variant c.334G>A p.Gly112Arg	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1441604	snp	C	T	missense_variant c.140G>A p.Ser47Asn	hslJ	lipoprotein implicated in Novobiocin resistance
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630642	snp	G	A	missense_variant c.317G>A p.Arg106His	yfgI	nalidixic acid resistance protein YfgI
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

ID015at48

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1006886	snp	C	T	missense_variant c.715G>A p.Gly239Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007267	snp	C	T	missense_variant c.334G>A p.Gly112Arg	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1441604	snp	C	T	missense_variant c.140G>A p.Ser47Asn	hslJ	lipoprotein implicated in Novobiocin resistance
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630642	snp	G	A	missense_variant c.317G>A p.Arg106His	yfgI	nalidixic acid resistance protein YfgI
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

ID016at24

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635811	snp	G	A	missense_variant c.971G>A p.Arg324Gln	yhiM	inner membrane protein with a role in acid resistance

ID017at48

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635811	snp	G	A	missense_variant c.971G>A p.Arg324Gln	yhiM	inner membrane protein with a role in acid resistance

ID018at24

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318124	snp	A	G	missense_variant c.196T>C p.Tyr66His	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
743316	snp	G	C	missense_variant c.490G>C p.Val164Leu	ybgI	radiation resistance protein YbgI
1006557	snp	C	T	missense_variant c.1044G>A p.Met348Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441532	snp	C	T	missense_variant c.212G>A p.Ser71Asn	hslJ	lipoprotein implicated in Novobiocin resistance
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227353	snp	A	G	missense_variant c.1406T>C p.Leu469Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227422	snp	G	C	missense_variant c.1337C>G p.Pro446Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227443	snp	G	C	missense_variant c.1316C>G p.Ala439Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227476	snp	C	G	missense_variant c.1283G>C p.Arg428Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227641	snp	T	A	missense_variant c.1118A>T p.Gln373Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227767	snp	G	A	missense_variant c.992C>T p.Ser331Phe	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227872	snp	G	C	missense_variant c.887C>G p.Pro296Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227968	snp	A	G	missense_variant c.791T>C p.Leu264Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228004	snp	C	A	missense_variant c.755G>T p.Gly252Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228444	snp	T	G	missense_variant c.315A>C p.Arg105Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228567	snp	T	C	missense_variant c.192A>G p.Ile64Met	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228649	snp	G	A	missense_variant c.110C>T p.Pro37Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228654	snp	T	G	missense_variant c.105A>C p.Gln35His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630612	snp	A	G	missense_variant c.287A>G p.Lys96Arg	yfgI	nalidixic acid resistance protein YfgI
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
3870310	snp	T	A	missense_variant c.934T>A p.Trp312Arg	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103326	snp	G	A	missense_variant c.505G>A p.Val169Met	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID020at24

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID021at24

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007259	snp	G	C	missense_variant c.342C>G p.Phe114Leu	ycbX	6-N-hydroxylaminopurine resistance protein
1216436	snp	C	T	missense_variant c.68C>T p.Ser23Leu	ariR	regulator of acid resistance, influenced by indole
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1501490	snp	T	G	missense_variant c.918T>G p.Phe306Leu	tehA	tellurite resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228307	snp	C	T	missense_variant c.452G>A p.Gly151Asp	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228496	snp	A	C	missense_variant c.263T>G p.Phe88Cys	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

ID025III

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID025II

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635811	snp	G	A	missense_variant c.971G>A p.Arg324Gln	yhiM	inner membrane protein with a role in acid resistance

ID025I

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635811	snp	G	A	missense_variant c.971G>A p.Arg324Gln	yhiM	inner membrane protein with a role in acid resistance

ID026

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635811	snp	G	A	missense_variant c.971G>A p.Arg324Gln	yhiM	inner membrane protein with a role in acid resistance

ID027

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635811	snp	G	A	missense_variant c.971G>A p.Arg324Gln	yhiM	inner membrane protein with a role in acid resistance

ID031

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318124	snp	A	G	missense_variant c.196T>C p.Tyr66His	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
1006557	snp	C	T	missense_variant c.1044G>A p.Met348Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1006753	snp	A	G	missense_variant c.848T>C p.Ile283Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1169089	snp	C	A	missense_variant c.17C>A p.Thr6Asn	bhsA	DUF1471 domain-containing multiple stress resistance outer membrane protein BhsA
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620106	snp	C	A	missense_variant c.118C>A p.Pro40Thr	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227429	snp	C	T	missense_variant c.1330G>A p.Glu444Lys	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	G	missense_variant c.1307T>C p.Leu436Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227570	snp	C	T	missense_variant c.1189G>A p.Gly397Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227968	snp	A	G	missense_variant c.791T>C p.Leu264Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228004	snp	C	A	missense_variant c.755G>T p.Gly252Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228444	snp	T	G	missense_variant c.315A>C p.Arg105Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228530	snp	T	C	missense_variant c.229A>G p.Thr77Ala	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228556	snp	A	G	missense_variant c.203T>C p.Leu68Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228628	snp	G	A	missense_variant c.131C>T p.Ala44Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228689	snp	G	T	missense_variant c.70C>A p.Pro24Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3869486	snp	G	A	missense_variant c.110G>A p.Cys37Tyr	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
3870310	snp	T	A	missense_variant c.934T>A p.Trp312Arg	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID032I

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
742927	snp	C	T	missense_variant c.101C>T p.Thr34Met	ybgI	radiation resistance protein YbgI
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1006933	snp	C	T	missense_variant c.668G>A p.Gly223Asp	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007131	snp	T	G	missense_variant c.470A>C p.Asp157Ala	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501299	snp	C	T	missense_variant c.727C>T p.Arg243Cys	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227908	snp	G	A	missense_variant c.851C>T p.Ala284Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228241	snp	C	T	missense_variant c.518G>A p.Gly173Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228277	snp	C	T	missense_variant c.482G>A p.Arg161Gln	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228406	snp	C	A	missense_variant c.353G>T p.Arg118Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID033I

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227588	snp	G	A	missense_variant c.1171C>T p.Arg391Trp	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869407	snp	C	A	missense_variant c.31C>A p.Leu11Ile	cbrA	colicin M resistance protein
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

ID034II

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635811	snp	G	A	missense_variant c.971G>A p.Arg324Gln	yhiM	inner membrane protein with a role in acid resistance

ID034I

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635811	snp	G	A	missense_variant c.971G>A p.Arg324Gln	yhiM	inner membrane protein with a role in acid resistance

ID037

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1216484	snp	C	A	missense_variant c.116C>A p.Thr39Asn	ariR	regulator of acid resistance, influenced by indole
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1501490	snp	T	G	missense_variant c.918T>G p.Phe306Leu	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620058	snp	A	C	missense_variant c.70A>C p.Thr24Pro	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635508	snp	A	G	missense_variant c.668A>G p.His223Arg	yhiM	inner membrane protein with a role in acid resistance
3869815	snp	A	T	missense_variant c.439A>T p.Thr147Ser	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein

ID043I

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
743181	snp	A	T	missense_variant c.355A>T p.Thr119Ser	ybgI	radiation resistance protein YbgI
1007522	snp	C	T	missense_variant c.79G>A p.Val27Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1007576	snp	T	C	missense_variant c.25A>G p.Ile9Val	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441506	snp	C	T	missense_variant c.238G>A p.Glu80Lys	hslJ	lipoprotein implicated in Novobiocin resistance
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620022	snp	C	T	missense_variant c.34C>T p.Leu12Phe	marB	multiple antibiotic resistance protein
1620037	snp	G	A	missense_variant c.49G>A p.Ala17Thr	marB	multiple antibiotic resistance protein
1620046	snp	G	A	missense_variant c.58G>A p.Val20Ile	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227326	snp	G	A	missense_variant c.1433C>T p.Ala478Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227422	snp	G	C	missense_variant c.1337C>G p.Pro446Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227443	snp	G	C	missense_variant c.1316C>G p.Ala439Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227563	snp	G	A	missense_variant c.1196C>T p.Pro399Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227668	snp	A	G	missense_variant c.1091T>C p.Val364Ala	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228190	snp	G	A	missense_variant c.569C>T p.Ala190Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228444	snp	T	G	missense_variant c.315A>C p.Arg105Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228502	snp	C	T	missense_variant c.257G>A p.Ser86Asn	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630356	snp	G	A	missense_variant c.31G>A p.Ala11Thr	yfgI	nalidixic acid resistance protein YfgI
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3635277	snp	C	T	missense_variant c.437C>T p.Thr146Ile	yhiM	inner membrane protein with a role in acid resistance
3635534	snp	T	A	missense_variant c.694T>A p.Phe232Ile	yhiM	inner membrane protein with a role in acid resistance
3869635	snp	C	T	missense_variant c.259C>T p.Leu87Phe	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870080	snp	G	A	missense_variant c.704G>A p.Ser235Asn	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4103121	snp	G	T	missense_variant c.300G>T p.Met100Ile	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID045

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
317767	snp	G	A	missense_variant c.553C>T p.Arg185Cys	rclC	reactive chlorine species resistance protein C
317874	snp	C	T	missense_variant c.446G>A p.Gly149Asp	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1441734	snp	C	G	missense_variant c.10G>C p.Val4Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1500807	snp	C	A	missense_variant c.235C>A p.Leu79Met	tehA	tellurite resistance protein
1501409	snp	T	A	missense_variant c.837T>A p.Asp279Glu	tehA	tellurite resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein

ID047

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6408	snp	T	G	missense_variant c.52A>C p.Thr18Pro	yaaA	peroxide stress resistance protein YaaA
317736	snp	G	A	missense_variant c.584C>T p.Thr195Ile	rclC	reactive chlorine species resistance protein C
317780	snp	T	G	missense_variant c.540A>C p.Glu180Asp	rclC	reactive chlorine species resistance protein C
1006759	snp	G	A	missense_variant c.842C>T p.Ala281Val	ycbX	6-N-hydroxylaminopurine resistance protein
1006832	snp	C	T	missense_variant c.769G>A p.Val257Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441506	snp	C	T	missense_variant c.238G>A p.Glu80Lys	hslJ	lipoprotein implicated in Novobiocin resistance
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620022	snp	C	T	missense_variant c.34C>T p.Leu12Phe	marB	multiple antibiotic resistance protein
1620037	snp	G	A	missense_variant c.49G>A p.Ala17Thr	marB	multiple antibiotic resistance protein
1620046	snp	G	A	missense_variant c.58G>A p.Val20Ile	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227443	snp	G	C	missense_variant c.1316C>G p.Ala439Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227570	snp	C	T	missense_variant c.1189G>A p.Gly397Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228118	snp	G	A	missense_variant c.641C>T p.Pro214Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228190	snp	G	A	missense_variant c.569C>T p.Ala190Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228406	snp	C	A	missense_variant c.353G>T p.Arg118Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228530	snp	T	C	missense_variant c.229A>G p.Thr77Ala	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228701	snp	C	T	missense_variant c.58G>A p.Ala20Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630545	snp	G	A	missense_variant c.220G>A p.Ala74Thr	yfgI	nalidixic acid resistance protein YfgI
2630629	snp	G	C	missense_variant c.304G>C p.Glu102Gln	yfgI	nalidixic acid resistance protein YfgI
3635277	snp	C	T	missense_variant c.437C>T p.Thr146Ile	yhiM	inner membrane protein with a role in acid resistance
3635534	snp	T	A	missense_variant c.694T>A p.Phe232Ile	yhiM	inner membrane protein with a role in acid resistance
3869866	snp	C	T	missense_variant c.490C>T p.His164Tyr	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870058	snp	A	G	missense_variant c.682A>G p.Thr228Ala	cbrA	colicin M resistance protein
3870229	snp	G	A	missense_variant c.853G>A p.Gly285Arg	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4103121	snp	G	T	missense_variant c.300G>T p.Met100Ile	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID050

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6288	snp	C	T	missense_variant c.172G>A p.Gly58Ser	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
1500893	snp	C	G	missense_variant c.321C>G p.Cys107Trp	tehA	tellurite resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630545	snp	G	A	missense_variant c.220G>A p.Ala74Thr	yfgI	nalidixic acid resistance protein YfgI
2630629	snp	G	C	missense_variant c.304G>C p.Glu102Gln	yfgI	nalidixic acid resistance protein YfgI

ID051

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227767	snp	G	A	missense_variant c.992C>T p.Ser331Phe	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227890	snp	C	G	missense_variant c.869G>C p.Trp290Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227908	snp	G	A	missense_variant c.851C>T p.Ala284Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228444	snp	T	G	missense_variant c.315A>C p.Arg105Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3635534	snp	T	A	missense_variant c.694T>A p.Phe232Ile	yhiM	inner membrane protein with a role in acid resistance
3635595	snp	C	T	missense_variant c.755C>T p.Ala252Val	yhiM	inner membrane protein with a role in acid resistance
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein

ID052

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6408	snp	T	G	missense_variant c.52A>C p.Thr18Pro	yaaA	peroxide stress resistance protein YaaA
303216	snp	A	G	missense_variant c.226A>G p.Ile76Val	yagU	inner membrane protein that contributes to acid resistance
317780	snp	T	G	missense_variant c.540A>C p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
743202	snp	C	T	missense_variant c.376C>T p.Pro126Ser	ybgI	radiation resistance protein YbgI
1006759	snp	G	A	missense_variant c.842C>T p.Ala281Val	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007074	snp	A	G	missense_variant c.527T>C p.Val176Ala	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1216562	snp	G	A	missense_variant c.194G>A p.Ser65Asn	ariR	regulator of acid resistance, influenced by indole
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501518	snp	G	A	missense_variant c.946G>A p.Val316Ile	tehA	tellurite resistance protein
1501537	snp	T	C	missense_variant c.965T>C p.Val322Ala	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620037	snp	G	A	missense_variant c.49G>A p.Ala17Thr	marB	multiple antibiotic resistance protein
1620046	snp	G	A	missense_variant c.58G>A p.Val20Ile	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227422	snp	G	C	missense_variant c.1337C>G p.Pro446Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	G	missense_variant c.1307T>C p.Leu436Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227974	snp	G	A	missense_variant c.785C>T p.Ala262Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228256	snp	A	T	missense_variant c.503T>A p.Val168Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228418	snp	C	T	missense_variant c.341G>A p.Gly114Asp	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228530	snp	T	C	missense_variant c.229A>G p.Thr77Ala	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228668	snp	C	T	missense_variant c.91G>A p.Ala31Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635534	snp	T	A	missense_variant c.694T>A p.Phe232Ile	yhiM	inner membrane protein with a role in acid resistance
3869447	snp	G	A	missense_variant c.71G>A p.Gly24Asp	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870058	snp	A	G	missense_variant c.682A>G p.Thr228Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4103121	snp	G	T	missense_variant c.300G>T p.Met100Ile	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID057

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
317737	snp	T	C	missense_variant c.583A>G p.Thr195Ala	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103027	snp	C	T	missense_variant c.206C>T p.Ala69Val	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103116	snp	T	C	missense_variant c.295T>C p.Tyr99His	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID058

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
303016	snp	C	T	missense_variant c.26C>T p.Pro9Leu	yagU	inner membrane protein that contributes to acid resistance
303486	snp	G	C	missense_variant c.496G>C p.Val166Leu	yagU	inner membrane protein that contributes to acid resistance
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID066

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6339	snp	G	T	missense_variant c.121C>A p.Leu41Met	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007270	snp	T	G	missense_variant c.331A>C p.Ser111Arg	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1169131	snp	G	A	missense_variant c.59G>A p.Ser20Asn	bhsA	DUF1471 domain-containing multiple stress resistance outer membrane protein BhsA
1441734	snp	C	G	missense_variant c.10G>C p.Val4Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1500807	snp	C	A	missense_variant c.235C>A p.Leu79Met	tehA	tellurite resistance protein
1501409	snp	T	A	missense_variant c.837T>A p.Asp279Glu	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620037	snp	G	A	missense_variant c.49G>A p.Ala17Thr	marB	multiple antibiotic resistance protein
1620046	snp	G	A	missense_variant c.58G>A p.Val20Ile	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228032	snp	G	T	missense_variant c.727C>A p.Pro243Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630850	snp	C	A	missense_variant c.525C>A p.Asp175Glu	yfgI	nalidixic acid resistance protein YfgI
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

ID070

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630642	snp	G	A	missense_variant c.317G>A p.Arg106His	yfgI	nalidixic acid resistance protein YfgI

ID073

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620046	snp	G	A	missense_variant c.58G>A p.Val20Ile	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227476	snp	C	G	missense_variant c.1283G>C p.Arg428Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228100	snp	G	A	missense_variant c.659C>T p.Ala220Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228701	snp	C	T	missense_variant c.58G>A p.Ala20Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3635117	snp	G	A	missense_variant c.277G>A p.Ala93Thr	yhiM	inner membrane protein with a role in acid resistance
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870058	snp	A	G	missense_variant c.682A>G p.Thr228Ala	cbrA	colicin M resistance protein
3870160	snp	G	A	missense_variant c.784G>A p.Val262Ile	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870276	snp	A	C	missense_variant c.900A>C p.Leu300Phe	cbrA	colicin M resistance protein
4103389	snp	C	T	missense_variant c.568C>T p.Arg190Cys	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID081

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6288	snp	C	T	missense_variant c.172G>A p.Gly58Ser	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
1500893	snp	C	G	missense_variant c.321C>G p.Cys107Trp	tehA	tellurite resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630545	snp	G	A	missense_variant c.220G>A p.Ala74Thr	yfgI	nalidixic acid resistance protein YfgI
2630629	snp	G	C	missense_variant c.304G>C p.Glu102Gln	yfgI	nalidixic acid resistance protein YfgI

ID096I

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GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6288	snp	C	T	missense_variant c.172G>A p.Gly58Ser	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
1500893	snp	C	G	missense_variant c.321C>G p.Cys107Trp	tehA	tellurite resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630545	snp	G	A	missense_variant c.220G>A p.Ala74Thr	yfgI	nalidixic acid resistance protein YfgI
2630629	snp	G	C	missense_variant c.304G>C p.Glu102Gln	yfgI	nalidixic acid resistance protein YfgI

ID098

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007428	snp	G	A	missense_variant c.173C>T p.Thr58Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	G	missense_variant c.34A>G p.Thr12Ala	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1216562	snp	G	A	missense_variant c.194G>A p.Ser65Asn	ariR	regulator of acid resistance, influenced by indole
1500615	snp	G	A	missense_variant c.43G>A p.Gly15Ser	tehA	tellurite resistance protein
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501399	snp	G	T	missense_variant c.827G>T p.Ser276Ile	tehA	tellurite resistance protein
1501518	snp	G	A	missense_variant c.946G>A p.Val316Ile	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227353	snp	A	G	missense_variant c.1406T>C p.Leu469Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227510	snp	C	T	missense_variant c.1249G>A p.Ala417Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227560	snp	A	G	missense_variant c.1199T>C p.Val400Ala	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227566	snp	T	C	missense_variant c.1193A>G p.Gln398Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227872	snp	G	C	missense_variant c.887C>G p.Pro296Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228239	snp	G	A	missense_variant c.520C>T p.Arg174Trp	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630364	snp	A	T	missense_variant c.39A>T p.Leu13Phe	yfgI	nalidixic acid resistance protein YfgI
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3635534	snp	T	A	missense_variant c.694T>A p.Phe232Ile	yhiM	inner membrane protein with a role in acid resistance
3635595	snp	C	T	missense_variant c.755C>T p.Ala252Val	yhiM	inner membrane protein with a role in acid resistance
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870080	snp	G	A	missense_variant c.704G>A p.Ser235Asn	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
3870295	snp	C	A	missense_variant c.919C>A p.Leu307Ile	cbrA	colicin M resistance protein
4102964	snp	A	T	missense_variant c.143A>T p.Lys48Met	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID099

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869407	snp	C	A	missense_variant c.31C>A p.Leu11Ile	cbrA	colicin M resistance protein
3869698	snp	A	C	missense_variant c.322A>C p.Lys108Gln	cbrA	colicin M resistance protein
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

ID24

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635811	snp	G	A	missense_variant c.971G>A p.Arg324Gln	yhiM	inner membrane protein with a role in acid resistance

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Phylogenetic inference

Phylogenetic inference based on vcf SNPS

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)

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Antimicrobial Resistance Profiling

Field	Description
Contig	Contig name where the gene was found
Start	Start position of the gene within the contig
End	End position of the gene within the contig
Gene	Antibiotic resistance gene
Gaps	Gaps in subject (genome) and query (antibiotic resistance gene)
Coverage	Proportion (%) of the gene covered
Identity	Proportion (%) of exact nucleotide matches
Accession	Accesion number of the antibiotic resistance gene
Product	Antibiotic resistance gene product
Resistance	Antibiotic that the gene confers resistance to

Select the samples and the database

ID005zero

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00021	43	903	aac(3)-IIa_1	0/0	100	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00050	1540	2139	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00022	76948	77823	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00050	579	1409	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00003	55500	56732	mdf(A)_1	0/0	100	97.9	Y08743	mdf(A)

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00021	43	903	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00050	1540	2139	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00009	137147	140296	acrB	0/0	100.0	98.8	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00014	130171	133284	acrD	0/0	100.0	98.5	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00016	127223	128380	acrE	0/0	100.0	98.7	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00016	128392	131496	acrF	0/0	100.0	96.5	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00016	126162	126824	acrS	0/0	100.0	98.3	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	83334	84155	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00001	384476	385197	baeR	0/0	99.9	96.7	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00001	385194	386597	baeS	0/0	100.0	90.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00019	107883	109250	cpxA	0/0	99.6	98.6	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00006	15383	16015	CRP	0/0	100.0	99.0	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00022	76948	77823	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00024	49360	50532	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00024	50549	52087	emrB	0/0	100.0	98.1	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	86333	87388	emrK	0/0	100.0	97.3	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00024	48703	49233	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	87388	88926	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00010	138569	140212	eptA	0/0	100.0	91.1	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00009	140319	141512	Escherichia_coli_acrA	0/0	100.0	99.2	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00015	123964	125097	Escherichia_coli_ampC	0/0	100.0	98.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00009	47230	48387	Escherichia_coli_ampH	0/0	100.0	97.2	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00021	62521	62853	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00003	55500	56732	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	85195	85809	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	81597	85190	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00006	194273	195001	gadW	0/0	100.0	99.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00006	195370	196194	gadX	0/0	100.0	93.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00018	22172	22585	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00003	199372	200044	kdpE	0/0	99.3	95.8	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00006	225535	225918	marA	0/0	100.0	98.2	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00001	394210	395457	mdtA	0/0	100.0	95.8	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00001	391088	394210	mdtB	0/0	100.0	95.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00001	388010	391087	mdtC	0/0	100.0	93.9	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00006	189615	190772	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00006	190797	193910	mdtF	0/0	100.0	97.3	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00007	149242	150468	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00007	159099	160307	mdtH	0/0	100.0	98.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00010	108311	109342	mdtN	0/0	100.0	94.9	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00010	106260	108311	mdtO	0/0	100.0	97.1	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00010	104797	106263	mdtP	0/0	100.0	97.7	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00007	22609	24357	msbA	0/0	100.0	98.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00050	579	1409	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00001	187873	188841	pmrF	0/0	100.0	97.7	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00008	106533	108020	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	449838	451004	ugd	0/0	100.0	97.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00001	247373	249016	yojI	0/0	100.0	97.9	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00021	43	903	(AGly)aac3-IIa	0/0	100	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00015	123964	125097	(Bla)AmpC2_Ecoli	0/0	100	98.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00009	47230	48387	(Bla)ampH_Ecoli	0/0	100	97.2	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00022	76948	77823	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00050	579	1409	(Bla)blaOXA-1	0/0	100	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00003	253032	254933	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.5	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00021	43	903	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00050	1540	2094	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00022	76948	77823	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00015	123964	125097	blaEC-5	0/0	100	99.8	NG_049085.1	cephalosporin-hydrolyzing class C beta-lactamase EC-5	CEPHALOSPORIN
contig00050	579	1409	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00021	43	903	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00009	140319	141512	ACRA	0/0	100.0	99.2	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00009	137147	140296	ACRB	0/0	100.0	98.8	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00014	130171	133284	ACRD	0/0	100.0	98.5	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00016	127223	128380	ACRE	0/0	100.0	98.7	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00016	128392	131496	ACRF	0/0	100.0	96.5	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00016	126162	126824	ACRS	0/0	100.0	98.3	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00009	47230	48387	AMPH	0/0	100.0	97.2	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00001	407120	408972	ASMA	0/0	100.0	97.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00008	83334	84155	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00001	384476	385197	BAER	0/0	99.9	96.7	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00001	385194	386597	BAES	0/0	100.0	90.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	272484	273674	BCR	0/0	100.0	96.3	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00015	123964	125097	BLAEC	0/0	100.0	99.8	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00019	107188	107886	CPXAR	0/0	100.0	97.8	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00019	107883	109250	CPXAR	0/0	99.6	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00006	15383	16015	CRP	0/0	100.0	99.0	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00024	49360	50532	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00024	50549	52087	EMRB	0/0	100.0	98.1	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00004	212397	213587	EMRD	0/0	100.0	97.7	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	86225	87388	EMRK	0/0	100.0	97.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00024	48703	49233	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	87388	88926	EMRY	0/0	100.0	97.8	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00010	138569	140212	EPTA	0/0	100.0	91.1	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	81597	85190	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00006	194273	195001	GADW	0/0	100.0	99.7	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00006	195370	196194	GADX	0/0	100.0	93.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00018	22172	22585	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00003	199372	200044	KDPE	0/0	99.3	95.8	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00006	225529	225918	MARA	0/0	100.0	98.2	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00006	225080	225514	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00003	55500	56732	MDFA	0/0	100.0	98.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00001	394210	395457	MDTA	0/0	100.0	95.8	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00001	391088	394210	MDTB	0/0	100.0	95.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00001	388010	391087	MDTC	0/0	100.0	93.9	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00006	189615	190772	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00006	190797	193910	MDTF	0/0	100.0	97.3	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00007	149242	150468	MDTG	0/0	100.0	98.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00007	159099	160307	MDTH	0/0	100.0	98.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00005	208181	208510	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00005	207829	208194	MDTJ	0/0	100.0	97.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00005	125894	127266	MDTK	0/0	99.9	98.4	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00010	108311	109342	MDTN	0/0	100.0	94.9	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00010	106260	108311	MDTO	0/0	100.0	97.1	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00010	104797	106263	MDTP	0/0	100.0	97.7	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00007	22609	24357	MSBA	0/0	100.0	98.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00021	62521	62853	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00050	579	1409	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00003	253032	254933	PBP2	0/0	100.0	98.5	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	187873	188841	PMRF	0/0	100.0	97.7	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00002	234544	235413	ROBA	0/0	100.0	97.2	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00010	76047	76369	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00001	449838	451004	UGD	0/0	100.0	97.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00001	247373	249016	YOGI	0/0	100.0	97.9	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID008

Resfinder

## [1] "No antibiotic resistance genes from Resfinder database were found"

CARD

## [1] "No antibiotic resistance genes from CARD database were found"

ARG-ANNOT

## [1] "No antibiotic resistance genes from ARG-ANNOT database were found"

NCBI

## [1] "No antibiotic resistance genes from NCBI database were found"

MEGARES

## [1] "No antibiotic resistance genes from MEGARES database were found"

ID009

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00039	21173	21706	ant(2’’)-Ia_1	0/0	100	100.0	X04555	ant(2’’)-Ia	Gentamicin, Tobramycin
contig00039	23573	24400	blaOXA-2_1	0/0	100	100.0	DQ112222	blaOXA-2	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Ceftazidime, Piperacillin
contig00016	41554	42414	blaSHV-18_1	0/0	100	100.0	AF132290	blaSHV-18	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00118	12802	13221	fosA_6	0/0	100	95.2	ACZD01000244	fosA	Fosfomycin
contig00002	6240	7415	oqxA_1	0/0	100	93.5	EU370913	oqxA	Nalidixic_acid, Ciprofloxacin
contig00002	3064	6216	oqxB_1	0/0	100	95.4	EU370913	oqxB	Nalidixic_acid, Ciprofloxacin
contig00039	24850	25716	sul1_5	0/0	100	99.8	EU780013	sul1	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00039	21173	21706	ANT(2’’)-Ia	0/0	100.0	100.0	AF078527:3769-4303	Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii	aminoglycoside
contig00118	12802	13221	FosA5	0/0	100.0	94.3	KP143090.1:1619-1199	fosA5 is a fosfomycin resistance gene isolated from clinical strain of Escherichia coli E265. It is susceptible to amikacin tetracycline and imipenem and resistant to sulphonamide cephalosporins gentamicin ciprofloxacin chloramphenicol and streptomycin	fosfomycin
contig00004	3141	4334	Klebsiella_pneumoniae_acrA	2/3	99.8	95.1	AJ318073.1:793-1990	AcrA is a subunit of the AcrAB multidrug efflux system that in K. pneumoniae which is encoded by the acrRAB operon.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00246	2066	2395	Klebsiella_pneumoniae_KpnF	0/0	100.0	93.3	AP006725.1:2484238-2484568	KpnF subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan.	aminoglycoside, cephalosporin, macrolide, peptide, rifamycin, tetracycline
contig00335	550	1722	Klebsiella_pneumoniae_KpnG	0/0	100.0	94.6	ACWO01000051.1:22092-23265	KpnG consists of ~390 residues and resembles EmrA of E. coli. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin ceftazidime ciprofloxacin ertapenem erythromycin gentamicin imipenem ticarcillin norfloxacin polymyxin-B piperacillin spectinomycin tobramycin and streptomycin	aminoglycoside, carbapenem, cephalosporin, fluoroquinolone, macrolide, penam, penem, peptide
contig00053	1920	3044	Klebsiella_pneumoniae_OmpK37	0/0	100.0	92.5	AJ011502.1:300-1425	Klebsiella pneumoniae outer membrane porin protein. Is preferentially detected in porin-deficient strains. Functional characterization of this new porin revealed a narrower pore than those of porins OmpK35 and OmpK36 which did not allow penetration by certain beta-lactams. Also when a resistant strain expresses porin OmpK37 is less susceptible to cefotaxime and cefoxitin than when it is expressing either OmpK36 or OmpK35.	carbapenem, cephalosporin, cephamycin, monobactam, penam, penem
contig00002	6240	7415	oqxA	0/0	100.0	93.5	EU370913.1:46651-47827	RND efflux pump conferring resistance to fluoroquinolone	diaminopyrimidine, fluoroquinolone, glycylcycline, nitrofuran, tetracycline
contig00002	3064	6216	oqxB	0/0	100.0	95.4	EU370913.1:47850-51003	RND efflux pump conferring resistance to fluoroquinolone	diaminopyrimidine, fluoroquinolone, glycylcycline, nitrofuran, tetracycline
contig00039	23573	24400	OXA-2	0/0	100.0	100.0	M95287.4:2455-3283	OXA-2 is a beta-lactamase found in the Enterobacteriaceae family.	carbapenem, cephalosporin, penam
contig00016	41554	42414	SHV-18	0/0	100.0	100.0	AF132290:87-948	SHV-18 is an extended-spectrum beta-lactamase found in Acinetobacter baumannii and Klebsiella pneumoniae.	carbapenem, cephalosporin, penam
contig00039	24877	25716	sul1	0/0	100.0	99.9	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00039	21173	21706	(AGly)aadB	0/0	100	100.0	JQ690540:4275-4808	(AGly)aadB	NA
contig00039	21786	22574	(AGly)aphA16	0/0	100	100.0	NG_051908:101-889	(AGly)aphA16	NA
contig00104	5274	6434	(Bla)ampH	0/0	100	96.0	CP003785:4208384-4209544	(Bla)ampH	NA
contig00039	23573	24400	(Bla)blaOXA-2	0/0	100	100.0	HM131431:1-828	(Bla)blaOXA-2	NA
contig00016	41554	42414	(Bla)blaSHV-18	0/0	100	100.0	EU684753:1-861	(Bla)blaSHV-18	NA
contig00118	12802	13221	(Fcyn)FosA5	0/0	100	94.3	KP143090:1200-1619	(Fcyn)FosA5	NA
contig00002	6240	7415	(Flq)OqxA	0/0	100	93.5	EU370913:46652-47827	(Flq)OqxA	NA
contig00002	3064	6216	(Flq)OqxBgb	0/0	100	95.4	EU370913:47851-51003	(Flq)OqxBgb	NA
contig00039	24877	25716	(Sul)sul1	0/0	100	99.9	AF071413:6700-7539	(Sul)sul1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00039	21173	21706	ant(2’’)-Ia	0/0	100	100.0	NG_047387.1	aminoglycoside nucleotidyltransferase ANT(2’’)-Ia	GENTAMICIN, KANAMYCIN, TOBRAMYCIN
contig00039	21786	22574	aphA16	0/0	100	100.0	NG_051908.1	APH(3’) family aminoglycoside O-phosphotransferase AphA16	AMIKACIN, KANAMYCIN
contig00039	23573	24400	blaOXA-2	0/0	100	100.0	NG_049496.1	oxacillin-hydrolyzing class D beta-lactamase OXA-2	BETA-LACTAM
contig00016	41554	42414	blaSHV-18	0/0	100	100.0	NG_050047.1	class A extended-spectrum beta-lactamase SHV-18	CEPHALOSPORIN
contig00118	12802	13221	fosA_gen	0/0	100	95.2	NG_047881.1	FosA family fosfomycin resistance glutathione transferase	FOSFOMYCIN
contig00002	6240	7415	oqxA10	0/0	100	93.8	NG_050418.1	multidrug efflux RND transporter periplasmic adaptor subunit OqxA10	PHENICOL, QUINOLONE
contig00002	3064	6216	oqxB11	0/0	100	95.9	NG_050429.1	multidrug efflux RND transporter permease subunit OqxB11	PHENICOL, QUINOLONE
contig00039	24877	25716	sul1	0/0	100	100.0	NG_048081.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00004	3141	4334	ACRA	2/3	99.8	95.1	MEG_400	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00104	5274	6434	AMPH	0/0	100.0	96.0	MEG_730	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00039	21023	21706	ANT2-DPRIME	1/3	100.0	99.6	MEG_757	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT2-DPRIME	NA
contig00039	21786	22574	APH3-PRIME	0/0	100.0	100.0	MEG_1059	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-PRIME	NA
contig00042	23627	25450	ASMA	0/0	100.0	93.7	MEG_1179	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00015	18768	19466	CPXAR	0/0	100.0	97.0	MEG_2116	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00015	19463	20836	CPXAR	0/0	100.0	95.8	MEG_2115	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00036	27126	28068	CTX	0/0	100.0	95.5	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00137	3057	3999	CTX	0/0	100.0	95.9	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00118	12802	13221	FOSA	0/0	100.0	95.2	MEG_2991	Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA	NA
contig00005	53418	54649	KDEA	0/0	99.9	94.2	MEG_3447	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:KDEA	NA
contig00335	550	1722	KPN	0/0	100.0	94.6	MEG_3512	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:KPN	NA
contig00246	2066	2395	KPNF	0/0	100.0	93.3	MEG_3515	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:KPNF	NA
contig00058	18712	19803	KPNO	2/6	99.5	95.3	MEG_3516	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:KPNO	NA
contig00053	1920	3044	OMP37	0/0	100.0	92.5	MEG_4283	Drugs:betalactams:Mutant_porin_proteins:OMP37	NA
contig00002	6240	7415	OQXA	0/0	100.0	93.8	MEG_4326	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:OQXA	NA
contig00002	3064	6216	OQXB	0/0	100.0	95.9	MEG_4364	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:OQXB	NA
contig00039	23499	24625	OXA	0/0	95.5	99.5	MEG_5208	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00003	75561	77027	PHOR	0/0	100.0	93.6	MEG_5786	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_regulator:PHOR	NA
contig00039	24536	24883	QACEDELTA1	0/0	100.0	100.0	MEG_5829	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACEDELTA1	NA
contig00016	41457	42460	SHV	0/0	99.7	99.6	MEG_6428	Drugs:betalactams:Class_A_betalactamases:SHV	NA
contig00039	24876	25843	SULI	0/0	100.0	99.9	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA

ID011

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00195	94	882	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00255	8	844	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00102	8896	9771	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00193	522	1382	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00195	1013	1486	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00275	18	591	dfrA7_5	3/4	100.0	98.8	AJ419170	dfrA7	Trimethoprim
contig00039	1743	2975	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00260	67	988	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00102	3599	4255	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00219	162	1028	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00148	1335	2581	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00195	94	882	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00002	39532	42681	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00017	11081	14194	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00004	121480	124584	acrF	0/0	100.0	100.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00004	119523	120185	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00255	8	844	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00007	54644	55465	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00047	10640	11362	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00047	9240	10643	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00012	61077	62450	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00027	15387	16019	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00102	8896	9771	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00195	1013	1486	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00275	118	591	dfrA7	0/0	100.0	100.0	FJ854362:2338-2812	dfrA7 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00008	36546	37718	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00045	27995	29050	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00008	35889	36419	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00045	26457	27995	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00019	63251	64894	eptA	0/0	100.0	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00002	38316	39509	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00076	1	1129	Escherichia_coli_ampC	0/0	99.6	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00017	45575	46879	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00002	127675	128832	Escherichia_coli_ampH	0/0	100.0	99.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00039	1743	2975	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00045	29574	30188	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00045	30193	33786	evgS	0/0	100.0	99.7	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00041	2243	2971	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00041	1051	1875	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00049	33308	33721	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00095	7975	8652	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00008	37735	39273	Klebsiella_pneumoniae_KpnH	0/0	100.0	99.9	ASTU01000063.1:61248-62787	KpnH consists of ~511 residues resembles EmrB of E. coli and is probably a translocase in the KpnGH-TolC efflux protein in K. pneumoniae. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin ceftazidime ciprofloxacin ertapenem erythromycin gentamicin imipenem ticarcillin norfloxacin polymyxin-B piperacillin spectinomycin tobramycin and streptomycin.	aminoglycoside, carbapenem, cephalosporin, fluoroquinolone, macrolide, penam, penem, peptide
contig00034	12803	13186	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00047	347	1594	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00047	1594	4716	mdtB	0/0	100.0	97.6	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00047	4717	7794	mdtC	0/0	100.0	98.2	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00041	6472	7629	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00041	3334	6447	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00052	18399	19625	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00052	28254	29462	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00070	380	1591	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00005	21785	22816	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00005	22816	24867	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00005	24864	26330	mdtP	0/0	100.0	99.9	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00260	67	972	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00030	9608	10084	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00010	21707	23455	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00013	58318	59286	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00102	3599	4255	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00219	162	1001	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00193	522	1382	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00148	1335	2581	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00007	30779	32266	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00140	141	1784	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00195	94	882	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00255	8	844	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00017	45575	46879	(Bla)AmpC1_Ecoli	0/0	100.0	99.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00076	1	1129	(Bla)AmpC2_Ecoli	0/0	99.6	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00002	127675	128832	(Bla)ampH_Ecoli	0/0	100.0	99.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00102	8896	9771	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00193	522	1382	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00016	45993	47894	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00102	3599	4255	(Flq)qnr-S1	0/0	100.0	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00260	67	972	(MLS)mph(A)	0/0	100.0	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00219	162	1001	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00148	1307	2581	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00148	2612	3199	(Tet)tetR	0/0	90.3	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00195	1013	1486	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA
contig00275	118	591	(Tmt)dhfr7	0/0	100.0	100.0	X58425:594-1067	(Tmt)dhfr7	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00195	94	882	aadA5	0/0	100.0	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00255	8	844	aph(6)-Id	0/0	100.0	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00102	8896	9771	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00076	1	1129	blaEC	0/0	99.6	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00193	522	1382	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00195	1013	1486	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00275	118	591	dfrA7	0/0	100.0	100.0	NG_047737.1	trimethoprim-resistant dihydrofolate reductase DfrA7	TRIMETHOPRIM
contig00260	67	988	mph(A)	1/1	100.0	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00102	3599	4255	qnrS1	0/0	100.0	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00219	162	1001	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00148	1307	2506	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	38316	39509	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00002	39532	42681	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00017	11081	14194	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00004	121480	124584	ACRF	0/0	100.0	100.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00004	119523	120185	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00076	1	1129	AMPC	0/0	99.6	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00002	127675	128832	AMPH	0/0	100.0	99.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00195	94	882	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00255	8	844	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00055	9351	11203	ASMA	0/0	100.0	98.0	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00007	54644	55465	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00047	10640	11362	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00047	9240	10643	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00061	2095	3285	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00012	60382	61080	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00012	61077	62450	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00027	15387	16019	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00195	1013	1486	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00275	118	591	DFRA	0/0	100.0	100.0	MEG_2548	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00008	36546	37718	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00014	17254	18444	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00045	27995	29158	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00008	35889	36419	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00045	26457	27995	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00019	63251	64894	EPTA	0/0	100.0	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00045	30193	33786	EVGS	0/0	100.0	99.7	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00041	2243	2971	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00041	1051	1875	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00049	33308	33721	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00095	7975	8652	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00008	37735	39273	KPN	0/0	100.0	99.9	MEG_3513	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:KPN	NA
contig00034	12803	13192	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00034	13206	13640	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00039	1743	2975	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00047	347	1594	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00047	1594	4716	MDTB	0/0	100.0	97.6	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00047	4717	7794	MDTC	0/0	100.0	98.2	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00041	6472	7629	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00041	3334	6447	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00052	18399	19625	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00052	28254	29462	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00003	131924	132253	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00003	131572	131937	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00003	60170	61543	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00070	380	1591	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00005	21785	22816	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00005	22816	24867	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00005	24864	26330	MDTP	0/0	100.0	99.9	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00260	67	988	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00030	9608	10084	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00010	21707	23455	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00016	45993	47894	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00017	45575	46879	PBP4B	0/0	100.0	99.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00013	58318	59286	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00102	3599	4255	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00023	46359	47228	ROBA	0/0	100.0	98.8	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00005	48173	48495	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00219	35	1002	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00193	504	1744	TEM	0/0	97.9	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00148	1307	2581	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00140	141	1784	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID013

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00121	6460	7320	aac(3)-IId_1	0/0	100	99.9	EU022314	aac(3)-IId	Gentamicin, Tobramycin
contig00313	842	1645	aph(3’’)-Ib_5	0/0	100	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00313	6	842	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00708	562	1437	blaCTX-M-27_1	0/0	100	100.0	AY156923	blaCTX-M-27	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00134	2038	2898	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig01337	387	860	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00618	265	1028	erm(B)_18	2/2	100	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00134	6109	7042	mph(A)_2	2/13	100	98.3	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00313	1706	2521	sul2_3	0/0	100	100.0	HQ840942	sul2	Sulfamethoxazole
contig00499	850	2055	tet(B)_2	0/0	100	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00121	6460	7320	AAC(3)-IId	0/0	100.0	99.9	EU022314.1:0-861	AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig01076	509	1171	acrS	0/0	100.0	97.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00313	842	1645	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00313	6	842	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00626	1451	2270	bacA	0/0	99.8	97.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00298	3362	4083	baeR	0/0	99.9	97.4	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00298	1962	3365	baeS	0/0	100.0	90.1	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00708	562	1437	CTX-M-27	0/0	100.0	100.0	AY156923:0-876	CTX-M-27 is a beta-lactamase found in Escherichia coli	cephalosporin
contig01337	387	860	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00501	943	2115	emrA	0/0	100.0	97.8	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00013	19083	20138	emrK	0/0	100.0	96.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00501	286	816	emrR	0/0	100.0	99.2	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00013	17545	19083	emrY	0/0	100.0	98.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00618	291	1036	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00041	8903	10207	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	95.4	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00402	89	3663	evgS	0/0	99.5	96.3	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig01206	403	1131	gadW	0/0	100.0	96.8	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig01290	366	1132	gadX	0/0	93.0	93.7	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig01085	753	1166	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00077	7214	7891	kdpE	0/0	100.0	96.6	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00075	249	632	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00090	8496	9743	mdtA	0/0	100.0	95.6	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00273	268	1494	mdtG	0/0	100.0	98.0	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00236	3719	4927	mdtH	0/0	100.0	97.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00176	2303	3535	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00352	3072	4015	mdtN	0/0	91.5	97.8	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00563	645	2111	mdtP	0/0	100.0	96.5	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00134	6125	7042	mphA	1/12	100.0	98.6	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00145	2809	3285	mphB	0/0	100.0	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00313	1706	2521	sul2	0/0	100.0	99.6	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00134	2038	2898	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00499	850	2055	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00181	3394	4560	ugd	0/0	100.0	97.3	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00121	6460	7320	(AGly)aac3-IId	0/0	100	99.9	EU022314:1-861	(AGly)aac3-IId	NA
contig00313	842	1645	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00313	6	842	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00041	8903	10207	(Bla)AmpC1_Ecoli	0/0	100	95.4	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00708	562	1437	(Bla)blaCTX-M-27	0/0	100	100.0	AY156923:1-876	(Bla)blaCTX-M-27	NA
contig00134	2038	2898	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00618	291	1028	(MLS)erm(B)	0/0	100	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00134	6125	7042	(MLS)mph(A)	1/12	100	98.6	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00313	1706	2521	(Sul)sul2	0/0	100	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig00499	850	2055	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig01337	387	860	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00121	6460	7320	aac(3)-IId	0/0	100	100.0	NG_047251.1	aminoglycoside N-acetyltransferase AAC(3)-IId	GENTAMICIN
contig00313	842	1669	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00313	6	842	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00708	562	1437	blaCTX-M-27	0/0	100	100.0	NG_048976.1	class A extended-spectrum beta-lactamase CTX-M-27	CEPHALOSPORIN
contig00134	2038	2898	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig01337	387	860	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00618	291	1028	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00134	6109	7042	mph(A)	2/13	100	98.3	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00313	1706	2521	sul2	0/0	100	99.9	NG_048118.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00499	850	2055	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00121	6460	7320	AAC3	0/0	100.0	100.0	MEG_64	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig01076	509	1171	ACRS	0/0	100.0	97.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00313	842	1669	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00313	6	842	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00426	1170	3023	ASMA	0/0	100.0	98.0	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00626	1451	2270	BACA	0/0	99.8	97.2	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00298	3362	4083	BAER	0/0	99.9	97.4	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00298	1962	3365	BAES	0/0	100.0	90.1	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig01054	82	1272	BCR	0/0	100.0	96.7	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00708	540	1443	CTX	0/0	100.0	99.8	MEG_2401	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig01337	387	860	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00501	943	2115	EMRA	0/0	100.0	97.8	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00013	19083	20246	EMRK	0/0	100.0	96.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00501	286	816	EMRR	0/0	100.0	99.2	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00013	17545	19083	EMRY	0/0	100.0	98.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00618	265	1028	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00402	89	3663	EVGS	0/0	99.5	97.4	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig01206	403	1131	GADW	0/0	100.0	97.1	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig01290	366	1132	GADX	0/0	93.0	93.7	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig01085	753	1166	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00077	7214	7891	KDPE	0/0	100.0	96.6	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00075	243	632	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00090	8496	9743	MDTA	0/0	100.0	95.6	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00273	268	1494	MDTG	0/0	100.0	98.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00236	3719	4927	MDTH	0/0	100.0	97.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00449	148	513	MDTJ	0/0	100.0	98.6	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00176	2303	3535	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00352	3072	4015	MDTN	0/0	91.5	97.8	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00563	645	2111	MDTP	0/0	100.0	96.5	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00134	6109	7042	MPHA	2/13	100.0	98.3	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00145	2809	3285	MPHB	0/0	100.0	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00041	8903	10207	PBP4B	0/0	100.0	95.4	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00360	1212	2081	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00567	451	773	SOXS	0/0	99.7	97.5	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00313	1706	2521	SULII	0/0	100.0	100.0	MEG_6618	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00499	850	2055	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00181	3394	4560	UGD	0/0	100.0	97.3	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA

ID014at24

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig02215	28	888	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig01588	744	1343	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00690	1345	2133	aadA5_1	0/0	100.0	99.9	AF137361	aadA5	Streptomycin
contig00217	567	1370	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00620	1685	2560	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00063	5098	5958	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00614	183	665	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00690	2264	2737	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00063	357	1278	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00690	1	825	sul1_5	0/0	95.2	99.8	EU780013	sul1	Sulfamethoxazole
contig00217	1431	2246	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig01353	144	1390	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline
contig00212	1997	3202	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig02215	28	888	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig01588	744	1343	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00690	1345	2133	aadA5	0/0	100.0	99.9	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00872	1299	1961	acrS	0/0	100.0	99.1	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00217	567	1370	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00546	1993	2814	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00040	66	1469	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig01125	280	1683	baeS	0/0	100.0	90.5	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00590	14	1387	cpxA	0/0	100.0	98.3	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00620	1685	2560	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00614	183	665	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00690	2264	2737	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00901	1043	2215	emrA	0/0	100.0	99.3	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00901	386	916	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00306	281	1819	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00798	1	1604	eptA	0/0	97.6	99.3	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00960	1	1604	eptA	0/0	97.6	91.3	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00567	944	2077	Escherichia_coli_ampC	0/0	100.0	98.4	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00140	5012	6316	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.6	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00137	5343	6500	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00983	618	950	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig01875	533	1147	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00476	1	3514	evgS	0/0	97.8	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig01144	177	905	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig01154	178	906	gadW	0/0	100.0	100.0	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig01410	783	1563	gadX	0/0	94.7	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig01957	363	1143	gadX	0/0	94.7	93.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00136	3266	3943	kdpE	0/0	100.0	99.8	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00040	9082	10329	mdtA	0/0	100.0	100.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig01993	1	1126	mdtA	0/0	90.2	95.4	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00040	5960	9082	mdtB	0/0	100.0	98.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00040	2882	5959	mdtC	0/0	100.0	99.9	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00979	1	1133	mdtG	1/1	92.3	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00373	234	1442	mdtH	0/0	100.0	97.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00324	263	1474	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00060	4283	5314	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig01887	1	973	mdtN	0/0	94.3	96.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00060	5314	7365	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00060	7362	8828	mdtP	0/0	100.0	99.9	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00063	373	1278	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00020	3085	3561	mphB	0/0	100.0	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00082	3188	4936	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00690	1	798	sul1	0/0	95.0	99.9	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00217	1431	2246	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00063	5098	5958	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig01353	144	1390	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00212	1997	3202	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00680	587	1753	ugd	0/0	100.0	96.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig02215	28	888	(AGly)aac3-IIa	0/0	100	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00690	1345	2133	(AGly)aadA5	0/0	100	99.9	AF137361:64-852	(AGly)aadA5	NA
contig00217	567	1370	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00140	5012	6316	(Bla)AmpC1_Ecoli	0/0	100	98.6	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00567	944	2077	(Bla)AmpC2_Ecoli	0/0	100	98.4	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00137	5343	6500	(Bla)ampH_Ecoli	0/0	100	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00620	1685	2560	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00063	5098	5958	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00063	373	1278	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00690	1	798	(Sul)sul1	0/0	95	99.9	AF071413:6700-7539	(Sul)sul1	NA
contig00217	1431	2246	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig01353	116	1390	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00212	1997	3202	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00614	183	656	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA
contig00690	2264	2737	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig02215	28	888	aac(3)-IIe	0/0	100.0	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig01588	744	1298	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00690	1345	2133	aadA5	0/0	100.0	99.9	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00217	567	1394	aph(3’’)-Ib	0/0	100.0	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00620	1685	2560	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00567	944	2077	blaEC	0/0	100.0	99.9	NG_047496.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00063	5098	5958	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00614	183	656	dfrA14	0/0	100.0	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00690	2264	2737	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00063	357	1278	mph(A)	1/1	100.0	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00690	1	798	sul1	0/0	96.4	99.9	NG_048089.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00217	1431	2246	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig01353	116	1315	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE
contig00212	1997	3202	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig02215	28	888	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00872	1299	1961	ACRS	0/0	100.0	99.1	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00137	5343	6500	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00690	1345	2133	ANT3-DPRIME	0/0	100.0	99.9	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00217	567	1394	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00546	1993	2814	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00040	66	1469	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig01125	280	1683	BAES	0/0	100.0	90.5	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00567	944	2077	BLAEC	0/0	100.0	99.9	MEG_1276	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00590	14	1387	CPXAR	0/0	100.0	98.8	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00614	183	656	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00690	2264	2737	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00901	1043	2215	EMRA	0/0	100.0	99.3	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00901	386	916	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00306	281	1819	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00798	1	1604	EPTA	0/0	97.6	99.3	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00960	1	1604	EPTA	0/0	97.6	91.3	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00476	1	3514	EVGS	0/0	97.8	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig01144	177	905	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig01154	178	906	GADW	0/0	100.0	100.0	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig01410	783	1563	GADX	0/0	94.7	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig01957	363	1143	GADX	0/0	94.7	93.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00136	3266	3943	KDPE	0/0	100.0	99.8	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig01038	1256	1690	MARR	0/0	100.0	97.5	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig02349	256	690	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00040	9082	10329	MDTA	0/0	100.0	100.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig01993	1	1126	MDTA	0/0	90.2	95.4	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00040	5960	9082	MDTB	0/0	100.0	98.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00040	2882	5959	MDTC	0/0	100.0	99.9	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00979	1	1133	MDTG	1/1	92.3	99.8	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00373	234	1442	MDTH	0/0	100.0	97.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig01531	65	394	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig02284	674	979	MDTI	0/0	92.7	99.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00796	1232	2488	MDTK	0/0	91.5	98.9	MEG_3758	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00324	263	1474	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00060	4283	5314	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig01887	1	973	MDTN	0/0	94.3	96.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00060	5314	7365	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00060	7362	8828	MDTP	0/0	100.0	99.9	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00063	357	1278	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00020	3085	3561	MPHB	0/0	100.0	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00082	3188	4936	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00983	618	950	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00140	5012	6316	PBP4B	0/0	100.0	98.6	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00958	459	1328	ROBA	0/0	100.0	98.8	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00221	2037	2359	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00690	1	885	SULI	0/0	95.5	99.9	MEG_6616	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00217	1431	2246	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00063	5080	6325	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig01353	116	1390	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00212	1997	3202	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00212	3996	4412	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00680	587	1753	UGD	0/0	100.0	96.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA

ID015HW

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00077	901	1702	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00024	79762	80637	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00076	5984	6643	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig00077	6	503	dfrA12_8	0/0	100.0	99.8	AM040708	dfrA12	Trimethoprim
contig00084	2247	3010	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00001	25629	26861	mdf(A)_1	0/0	100.0	98.5	Y08743	mdf(A)
contig00084	161	1091	mph(A)_2	2/10	100.0	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00077	2180	3046	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00086	800	2005	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00077	923	1702	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00010	89029	92178	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00002	101962	105075	acrD	0/0	100.0	98.9	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00003	223403	224560	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	224572	227676	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	222342	223004	acrS	0/0	100.0	99.4	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	13409	14228	bacA	0/0	99.8	98.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00018	65847	66569	baeR	0/0	100.0	99.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00018	64447	65850	baeS	0/0	100.0	99.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00076	5984	6643	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00029	22407	23780	cpxA	0/0	100.0	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00005	15387	16019	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00024	79762	80637	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00077	6	503	dfrA12	0/0	100.0	99.8	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00066	5291	6463	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00066	3736	5274	emrB	0/0	100.0	99.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00002	10208	11263	emrK	0/0	100.0	99.2	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00066	6590	7120	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00002	8670	10208	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00031	18311	19954	eptA	0/0	100.0	99.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00084	2273	3018	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00010	92201	93394	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00032	48509	49642	Escherichia_coli_ampC	0/0	100.0	97.5	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00002	69540	70844	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00010	683	1840	Escherichia_coli_ampH	0/0	100.0	99.2	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00001	25629	26861	Escherichia_coli_mdfA	0/0	100.0	96.9	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00002	11787	12401	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00002	12406	15999	evgS	0/0	100.0	99.6	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00042	31471	32199	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00042	32567	33391	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00004	173845	174258	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00012	7933	8605	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00030	40685	41068	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00018	55587	56834	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00018	56834	59956	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00018	59957	63034	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00042	26813	27970	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00042	27995	31108	mdtF	0/0	100.0	98.5	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00025	38609	39835	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00025	28770	29978	mdtH	0/0	100.0	98.5	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00053	356	1588	mdtM	0/0	100.0	96.8	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00016	10888	11919	mdtN	0/0	100.0	98.1	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00016	11919	13970	mdtO	0/0	100.0	98.3	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00016	13967	15433	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00084	189	1091	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00002	126351	126825	mphB	0/0	99.6	97.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	152597	154345	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00007	32303	33271	pmrF	0/0	100.0	99.5	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00077	2207	3046	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00086	800	2005	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00036	36177	37664	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00019	14595	16238	yojI	0/0	100.0	98.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00077	923	1702	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00002	69540	70844	(Bla)AmpC1_Ecoli	0/0	100.0	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00032	48509	49642	(Bla)AmpC2_Ecoli	0/0	100.0	97.5	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00010	683	1840	(Bla)ampH_Ecoli	0/0	100.0	99.2	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00024	79762	80637	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00012	60394	62295	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00084	2273	3010	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00084	189	1091	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00076	5984	6643	(Phe)catA1	0/0	100.0	99.8	V00622:244-903	(Phe)catA1	NA
contig00077	2207	3046	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00086	800	2005	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00077	6	503	(Tmt)dfrA12	0/0	100.0	99.8	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00077	911	1702	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00024	79762	80637	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00032	48509	49642	blaEC-13	0/0	100	99.9	NG_049079.1	class C extended-spectrum beta-lactamase EC-13	CEPHALOSPORIN
contig00076	5984	6643	catA1	0/0	100	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00077	6	503	dfrA12	0/0	100	99.8	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00084	2273	3010	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00084	161	1091	mph(A)	2/10	100	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00077	2207	3046	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00086	800	2005	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	92201	93394	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00010	89029	92178	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00002	101962	105075	ACRD	0/0	100.0	98.9	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00003	223403	224560	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00003	224572	227676	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00003	222342	223004	ACRS	0/0	100.0	99.4	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00010	683	1840	AMPH	0/0	100.0	99.2	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00077	901	1702	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00018	41800	43652	ASMA	0/0	100.0	98.4	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00003	13409	14228	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00018	65847	66569	BAER	0/0	100.0	99.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00018	64447	65850	BAES	0/0	100.0	99.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00019	41510	42700	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00032	48509	49642	BLAEC	0/0	100.0	99.9	MEG_1280	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00076	5984	6648	CATA	0/0	99.1	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00029	21712	22410	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00029	22407	23780	CPXAR	0/0	100.0	99.5	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00005	15387	16019	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00018	92803	93691	CTX	0/0	100.0	97.4	MEG_2430	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00077	6	503	DFRA	0/0	100.0	99.8	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00066	5291	6463	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00066	3736	5274	EMRB	0/0	100.0	99.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00014	22228	23418	EMRD	0/0	100.0	99.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00002	10208	11371	EMRK	0/0	100.0	99.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00066	6590	7120	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00002	8670	10208	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00031	18311	19954	EPTA	0/0	100.0	99.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00084	2247	3010	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00002	12406	15999	EVGS	0/0	100.0	99.6	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00042	31471	32199	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00042	32567	33391	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00004	173845	174258	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00012	7933	8605	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00030	40679	41068	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00030	40231	40665	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00001	25629	26861	MDFA	0/0	100.0	98.5	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00018	55587	56834	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00018	56834	59956	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00018	59957	63034	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00042	26813	27970	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00042	27995	31108	MDTF	0/0	100.0	98.5	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00025	38609	39835	MDTG	0/0	100.0	99.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00025	28770	29978	MDTH	0/0	100.0	98.5	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00021	35394	35723	MDTI	0/0	100.0	99.1	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00021	35042	35407	MDTJ	0/0	100.0	99.7	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00017	65582	66955	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00053	356	1588	MDTM	0/0	100.0	96.8	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00016	10888	11919	MDTN	0/0	100.0	98.1	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00016	11919	13970	MDTO	0/0	100.0	98.3	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00016	13967	15433	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00084	161	1091	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00002	126351	126825	MPHB	0/0	99.6	97.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	152597	154345	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00012	60394	62295	PBP2	0/0	100.0	99.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00002	69540	70844	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00007	32303	33271	PMRF	0/0	100.0	99.5	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00027	11922	12791	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00016	37049	37372	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00077	2206	3173	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00086	800	2005	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00086	2799	3215	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00019	14595	16238	YOGI	0/0	100.0	98.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID015at48

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00085	901	1702	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00006	2052	2927	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00087	1420	2079	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig00085	6	503	dfrA12_8	0/0	100.0	99.8	AM040708	dfrA12	Trimethoprim
contig00096	2354	3117	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00037	18321	19553	mdf(A)_1	0/0	100.0	98.5	Y08743	mdf(A)
contig00096	268	1198	mph(A)_2	2/10	100.0	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00085	2180	3046	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00098	800	2005	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00085	923	1702	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00014	89029	92178	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	123264	126377	acrD	0/0	100.0	98.9	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00002	223403	224560	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00002	224572	227676	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00002	222342	223004	acrS	0/0	100.0	99.4	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00002	13409	14228	bacA	0/0	99.8	98.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00013	65847	66569	baeR	0/0	100.0	99.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00013	64447	65850	baeS	0/0	100.0	99.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00087	1420	2079	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00056	22407	23780	cpxA	0/0	100.0	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00007	15387	16019	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00006	2052	2927	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00085	6	503	dfrA12	0/0	100.0	99.8	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00055	5175	6347	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00055	3620	5158	emrB	0/0	100.0	99.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	31510	32565	emrK	0/0	100.0	99.2	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00055	6474	7004	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	29972	31510	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00030	18346	19989	eptA	0/0	100.0	99.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00096	2380	3125	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00014	92201	93394	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00031	49645	50778	Escherichia_coli_ampC	0/0	100.0	97.5	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	90842	92146	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00014	683	1840	Escherichia_coli_ampH	0/0	100.0	99.2	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00037	18321	19553	Escherichia_coli_mdfA	0/0	100.0	96.9	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	33089	33703	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	33708	37301	evgS	0/0	100.0	99.6	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00020	31471	32199	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00020	32567	33391	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00018	10093	10506	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00045	8520	9192	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00028	40685	41068	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00013	55587	56834	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00013	56834	59956	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00013	59957	63034	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00020	26813	27970	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00020	27995	31108	mdtF	0/0	100.0	98.5	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00006	121340	122566	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00006	111501	112709	mdtH	0/0	100.0	98.5	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00019	52386	53618	mdtM	0/0	100.0	96.8	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00010	10863	11894	mdtN	0/0	100.0	98.1	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00010	11894	13945	mdtO	0/0	100.0	98.3	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00010	13942	15408	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00096	296	1198	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00001	147653	148127	mphB	0/0	99.6	97.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00003	31022	32770	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00011	16717	17685	pmrF	0/0	100.0	99.5	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00085	2207	3046	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00098	800	2005	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00035	36177	37664	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00032	30181	31824	yojI	0/0	100.0	98.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00085	923	1702	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00001	90842	92146	(Bla)AmpC1_Ecoli	0/0	100.0	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00031	49645	50778	(Bla)AmpC2_Ecoli	0/0	100.0	97.5	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00014	683	1840	(Bla)ampH_Ecoli	0/0	100.0	99.2	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00006	2052	2927	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00046	13699	15600	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00096	2380	3117	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00096	296	1198	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00087	1420	2079	(Phe)catA1	0/0	100.0	99.8	V00622:244-903	(Phe)catA1	NA
contig00085	2207	3046	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00098	800	2005	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00085	6	503	(Tmt)dfrA12	0/0	100.0	99.8	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00085	911	1702	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00006	2052	2927	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00031	49645	50778	blaEC-13	0/0	100	99.9	NG_049079.1	class C extended-spectrum beta-lactamase EC-13	CEPHALOSPORIN
contig00087	1420	2079	catA1	0/0	100	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00085	6	503	dfrA12	0/0	100	99.8	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00096	2380	3117	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00096	268	1198	mph(A)	2/10	100	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00085	2207	3046	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00098	800	2005	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00014	92201	93394	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00014	89029	92178	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00001	123264	126377	ACRD	0/0	100.0	98.9	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00002	223403	224560	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00002	224572	227676	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00002	222342	223004	ACRS	0/0	100.0	99.4	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00014	683	1840	AMPH	0/0	100.0	99.2	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00085	901	1702	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00013	41800	43652	ASMA	0/0	100.0	98.4	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00002	13409	14228	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00013	65847	66569	BAER	0/0	100.0	99.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00013	64447	65850	BAES	0/0	100.0	99.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00017	83075	84265	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00031	49645	50778	BLAEC	0/0	100.0	99.9	MEG_1280	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00087	1415	2079	CATA	0/0	99.1	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00056	21712	22410	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00056	22407	23780	CPXAR	0/0	100.0	99.5	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	15387	16019	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00013	92803	93691	CTX	0/0	100.0	97.4	MEG_2430	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00085	6	503	DFRA	0/0	100.0	99.8	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00055	5175	6347	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00055	3620	5158	EMRB	0/0	100.0	99.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00009	22228	23418	EMRD	0/0	100.0	99.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	31510	32673	EMRK	0/0	100.0	99.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00055	6474	7004	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	29972	31510	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00030	18346	19989	EPTA	0/0	100.0	99.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00096	2354	3117	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00001	33708	37301	EVGS	0/0	100.0	99.6	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00020	31471	32199	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00020	32567	33391	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00018	10093	10506	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00045	8520	9192	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00028	40679	41068	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00028	40231	40665	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00037	18321	19553	MDFA	0/0	100.0	98.5	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00013	55587	56834	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00013	56834	59956	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00013	59957	63034	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00020	26813	27970	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00020	27995	31108	MDTF	0/0	100.0	98.5	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00006	121340	122566	MDTG	0/0	100.0	99.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00006	111501	112709	MDTH	0/0	100.0	98.5	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00022	35375	35704	MDTI	0/0	100.0	99.1	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00022	35023	35388	MDTJ	0/0	100.0	99.7	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00051	31774	33147	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00019	52386	53618	MDTM	0/0	100.0	96.8	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00010	10863	11894	MDTN	0/0	100.0	98.1	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00010	11894	13945	MDTO	0/0	100.0	98.3	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00010	13942	15408	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00096	268	1198	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00001	147653	148127	MPHB	0/0	99.6	97.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00003	31022	32770	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00046	13699	15600	PBP2	0/0	100.0	99.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	90842	92146	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00011	16717	17685	PMRF	0/0	100.0	99.5	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00064	11922	12791	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00010	37024	37347	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00085	2206	3173	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00098	800	2005	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00098	2799	3215	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00032	30181	31824	YOGI	0/0	100.0	98.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID016at24

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00089	2721	3522	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00075	371	1246	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00089	1826	2323	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00128	263	1026	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00009	30137	31369	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00139	68	998	mph(A)_2	2/10	100.0	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00089	4000	4866	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00123	850	2055	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00089	2743	3522	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00001	99712	102861	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00068	11538	14651	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00058	8289	9446	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00058	5173	8277	acrF	0/0	100.0	99.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00058	9845	10507	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	90705	91526	bacA	0/0	100.0	99.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00049	29821	30543	baeR	0/0	100.0	99.6	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00049	28421	29824	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00012	48374	49747	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00010	15201	15833	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00075	371	1246	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00089	1826	2323	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00003	90366	91538	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00003	91555	93093	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00017	1067	2122	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00003	89709	90239	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00030	7608	9251	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00128	289	1034	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00001	98496	99689	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	107745	108878	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00017	65523	66827	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00001	187826	188983	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00009	30137	31369	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00017	2646	3260	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00017	3265	6858	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00040	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00040	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00059	24580	24993	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00019	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00050	31344	31727	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00049	19561	20808	mdtA	0/0	100.0	97.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00049	20808	23930	mdtB	0/0	100.0	99.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00049	23931	27008	mdtC	0/0	100.0	99.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00040	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00040	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00002	159289	160515	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00002	169144	170352	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00063	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00011	21720	22751	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00011	22751	24802	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00011	24799	26265	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00139	68	970	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00054	17756	18232	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00002	12783	14531	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00004	62210	63178	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00089	4027	4866	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00123	850	2055	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00006	66840	68327	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00004	2107	3750	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00089	2743	3522	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00017	65523	66827	(Bla)AmpC1_Ecoli	0/0	100.0	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00005	107745	108878	(Bla)AmpC2_Ecoli	0/0	100.0	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00001	187826	188983	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00075	371	1246	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00019	60155	62056	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00128	289	1026	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00139	68	970	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00089	4027	4866	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00123	850	2055	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00089	1826	2323	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00089	2731	3522	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00075	371	1246	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00005	107745	108878	blaEC	0/0	100	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00089	1826	2323	dfrA12	0/0	100	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00128	289	1026	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00139	68	998	mph(A)	2/10	100	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00089	4027	4866	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00123	850	2055	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00001	98496	99689	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00001	99712	102861	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00068	11538	14651	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00058	8289	9446	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00058	5173	8277	ACRF	0/0	100.0	99.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00058	9845	10507	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00005	107745	108878	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00001	187826	188983	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00089	2721	3522	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00049	5770	7622	ASMA	0/0	100.0	97.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00006	90705	91526	BACA	0/0	100.0	99.9	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00049	29821	30543	BAER	0/0	100.0	99.6	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00049	28421	29824	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00020	49210	50400	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00012	47679	48377	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00012	48374	49747	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00010	15201	15833	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00143	62	1004	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00089	1826	2323	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00003	90366	91538	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00003	91555	93093	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00007	87171	88361	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00017	1067	2230	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00003	89709	90239	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00030	7608	9251	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00128	263	1026	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00017	3265	6858	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00040	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00040	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00059	24580	24993	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00019	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00050	31338	31727	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00050	30890	31324	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00009	30137	31369	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00049	19561	20808	MDTA	0/0	100.0	97.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00049	20808	23930	MDTB	0/0	100.0	99.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00049	23931	27008	MDTC	0/0	100.0	99.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00040	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00040	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00002	159289	160515	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00002	169144	170352	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00048	1757	2086	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00048	2073	2438	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00022	31959	33332	MDTK	0/0	100.0	98.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00063	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00011	21720	22751	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00011	22751	24802	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00011	24799	26265	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00139	68	998	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00054	17756	18232	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00002	12783	14531	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00019	60155	62056	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00017	65523	66827	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00004	62210	63178	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00008	38665	39534	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00011	47882	48205	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00089	4026	4993	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00123	850	2055	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00004	2107	3750	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID017at48

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00152	2721	3522	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00190	1684	2559	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00187	2039	2899	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00152	1826	2323	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00199	263	1026	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00017	30174	31406	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00152	4000	4866	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00186	850	2055	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00152	2743	3522	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00006	39318	42467	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00066	12933	16046	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00137	5381	8485	acrF	0/0	100.0	99.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00077	20439	21101	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	65835	66656	bacA	0/0	100.0	99.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00095	10772	11494	baeR	0/0	100.0	99.6	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00095	9372	10775	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00005	31213	32586	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00074	14885	15517	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00190	1684	2559	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00152	1826	2323	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00082	14502	15674	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00082	15691	17229	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00043	1067	2122	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00082	13845	14375	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00134	422	2065	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00199	289	1034	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00006	38102	39295	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00002	103325	104458	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00068	19827	21131	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00012	35901	37058	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00017	30174	31406	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00043	2646	3260	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00043	3265	6858	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00046	1586	2314	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00046	394	1218	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00065	22020	22433	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00054	8962	9639	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00127	6406	6789	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00095	512	1759	mdtA	0/0	100.0	97.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00095	1759	4881	mdtB	0/0	100.0	99.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00095	4882	7959	mdtC	0/0	100.0	99.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00046	5815	6972	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00046	2677	5790	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00030	16606	17832	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00030	26461	27669	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00069	262	1473	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00024	20208	21239	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00024	21239	23290	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00024	23287	24753	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00113	7732	8208	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00023	19048	20796	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00001	41659	42627	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00152	4027	4866	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00187	2039	2899	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00186	850	2055	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00004	89034	90521	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00084	16770	18413	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00152	2743	3522	(AGly)aadA2	0/0	100	99.9	X68227:66-945	(AGly)aadA2	NA
contig00068	19827	21131	(Bla)AmpC1_Ecoli	0/0	100	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00002	103325	104458	(Bla)AmpC2_Ecoli	0/0	100	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00012	35901	37058	(Bla)ampH_Ecoli	0/0	100	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00190	1684	2559	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00187	2039	2899	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00136	3245	5146	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00199	289	1026	(MLS)erm(B)	0/0	100	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00152	4027	4866	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00186	850	2055	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00152	1826	2323	(Tmt)dfrA12	0/0	100	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00152	2731	3522	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00190	1684	2559	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00002	103325	104458	blaEC	0/0	100	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00187	2039	2899	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00152	1826	2323	dfrA12	0/0	100	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00199	289	1026	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00152	4027	4866	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00186	850	2055	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00006	38102	39295	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00006	39318	42467	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00066	12933	16046	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00137	5381	8485	ACRF	0/0	100.0	99.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00077	20439	21101	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00002	103325	104458	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00012	35901	37058	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00152	2721	3522	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00093	11224	13076	ASMA	0/0	100.0	97.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00004	65835	66656	BACA	0/0	100.0	99.9	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00095	10772	11494	BAER	0/0	100.0	99.6	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00095	9372	10775	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00005	30518	31216	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00005	31213	32586	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00074	14885	15517	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00239	61	987	CTX	0/0	98.3	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00152	1826	2323	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00082	14502	15674	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00082	15691	17229	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00133	7141	8331	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00043	1067	2230	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00082	13845	14375	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00134	422	2065	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00199	263	1026	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00043	3265	6858	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00046	1586	2314	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00046	394	1218	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00065	22020	22433	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00054	8962	9639	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00127	6400	6789	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00127	5952	6386	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00017	30174	31406	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00095	512	1759	MDTA	0/0	100.0	97.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00095	1759	4881	MDTB	0/0	100.0	99.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00095	4882	7959	MDTC	0/0	100.0	99.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00046	5815	6972	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00046	2677	5790	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00030	16606	17832	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00030	26461	27669	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00048	1757	2086	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00048	2073	2438	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00019	24050	25423	MDTK	0/0	100.0	98.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00069	262	1473	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00024	20208	21239	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00024	21239	23290	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00024	23287	24753	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00113	7732	8208	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00023	19048	20796	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00136	3245	5146	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00068	19827	21131	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	41659	42627	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00015	19983	20852	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00024	46370	46693	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00152	4026	4993	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00186	850	2055	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00084	16770	18413	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID018at24

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00028	43	903	aac(3)-IIa_1	0/0	100	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00089	1540	2139	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00081	843	1646	aph(3’’)-Ib_5	0/0	100	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00081	7	843	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00064	2636	3511	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00089	579	1409	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00093	534	1394	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00073	33	506	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00008	16349	17581	mdf(A)_1	0/0	100	97.9	Y08743	mdf(A)
contig00099	68	989	mph(A)_2	1/1	100	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00081	1707	2522	sul2_3	0/0	100	100.0	HQ840942	sul2	Sulfamethoxazole
contig00080	770	1975	tet(B)_2	0/0	100	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00028	43	903	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00089	1540	2139	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00024	932	4081	acrB	0/0	100.0	98.8	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00019	28484	31597	acrD	0/0	100.0	98.5	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00010	127224	128381	acrE	0/0	100.0	98.7	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00010	128393	131497	acrF	0/0	100.0	96.5	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00010	126163	126825	acrS	0/0	100.0	98.3	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00081	843	1646	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00081	7	843	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00004	65932	66753	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00023	10384	11105	baeR	0/0	99.9	96.7	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00023	11102	12505	baeS	0/0	100.0	90.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00014	107883	109250	cpxA	0/0	99.6	98.6	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00005	15383	16015	CRP	0/0	100.0	99.0	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00064	2636	3511	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00073	33	506	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00030	60820	61992	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00030	62009	63547	emrB	0/0	100.0	98.1	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00017	65261	66316	emrK	0/0	100.0	97.3	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00030	60163	60693	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00017	63723	65261	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00022	42665	44308	eptA	0/0	100.0	91.1	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00024	4104	5297	Escherichia_coli_acrA	0/0	100.0	99.2	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00009	123964	125097	Escherichia_coli_ampC	0/0	100.0	98.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00025	22923	24080	Escherichia_coli_ampH	0/0	100.0	97.2	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00028	62521	62853	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00008	16349	17581	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00017	66840	67454	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00017	67459	71052	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00005	194273	195001	gadW	0/0	100.0	99.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00005	195370	196194	gadX	0/0	100.0	93.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00020	1686	2099	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00012	68376	69048	kdpE	0/0	99.3	95.8	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00043	8994	9377	marA	0/0	100.0	98.4	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00023	20118	21365	mdtA	0/0	100.0	95.8	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00023	16996	20118	mdtB	0/0	100.0	95.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00023	13918	16995	mdtC	0/0	100.0	93.9	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00005	189615	190772	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00005	190797	193910	mdtF	0/0	100.0	97.3	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00011	69746	70972	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00011	59907	61115	mdtH	0/0	100.0	98.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00022	12407	13438	mdtN	0/0	100.0	94.9	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00022	10356	12407	mdtO	0/0	100.0	97.1	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00022	8893	10359	mdtP	0/0	100.0	97.7	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00099	68	973	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00008	95721	97469	msbA	0/0	100.0	98.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00089	579	1409	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00003	185233	186201	pmrF	0/0	100.0	97.7	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00081	1707	2522	sul2	0/0	100.0	99.6	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00093	534	1394	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00080	770	1975	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00004	89131	90618	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00023	75746	76912	ugd	0/0	100.0	97.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00003	125058	126701	yojI	0/0	100.0	97.9	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00028	43	903	(AGly)aac3-IIa	0/0	100	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00081	843	1646	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00081	7	843	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00009	123964	125097	(Bla)AmpC2_Ecoli	0/0	100	98.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00025	22923	24080	(Bla)ampH_Ecoli	0/0	100	97.2	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00064	2636	3511	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00089	579	1409	(Bla)blaOXA-1	0/0	100	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00093	534	1394	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00012	122036	123937	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.5	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00099	68	973	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00081	1707	2522	(Sul)sul2	0/0	100	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig00080	770	1975	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00073	33	506	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00028	43	903	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00089	1540	2094	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00081	843	1670	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00081	7	843	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00064	2636	3511	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00009	123964	125097	blaEC-5	0/0	100	99.8	NG_049085.1	cephalosporin-hydrolyzing class C beta-lactamase EC-5	CEPHALOSPORIN
contig00089	579	1409	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00093	534	1394	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00073	33	506	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00099	68	989	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00081	1707	2522	sul2	0/0	100	99.9	NG_048118.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00080	770	1975	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00028	43	903	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00024	4104	5297	ACRA	0/0	100.0	99.2	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00024	932	4081	ACRB	0/0	100.0	98.8	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00019	28484	31597	ACRD	0/0	100.0	98.5	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00010	127224	128381	ACRE	0/0	100.0	98.7	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00010	128393	131497	ACRF	0/0	100.0	96.5	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00010	126163	126825	ACRS	0/0	100.0	98.3	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00025	22923	24080	AMPH	0/0	100.0	97.2	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00081	843	1670	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00081	7	843	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00023	33028	34880	ASMA	0/0	100.0	97.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00004	65932	66753	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00023	10384	11105	BAER	0/0	99.9	96.7	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00023	11102	12505	BAES	0/0	100.0	90.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00003	100400	101590	BCR	0/0	100.0	96.3	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00009	123964	125097	BLAEC	0/0	100.0	99.8	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00014	107188	107886	CPXAR	0/0	100.0	97.8	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00014	107883	109250	CPXAR	0/0	99.6	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00005	15383	16015	CRP	0/0	100.0	99.0	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00073	33	506	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00030	60820	61992	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00030	62009	63547	EMRB	0/0	100.0	98.1	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00002	201125	202315	EMRD	0/0	100.0	97.7	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00017	65261	66424	EMRK	0/0	100.0	97.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00030	60163	60693	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00017	63723	65261	EMRY	0/0	100.0	97.8	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00022	42665	44308	EPTA	0/0	100.0	91.1	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00017	67459	71052	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00005	194273	195001	GADW	0/0	100.0	99.7	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00005	195370	196194	GADX	0/0	100.0	93.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00020	1686	2099	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00012	68376	69048	KDPE	0/0	99.3	95.8	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00043	8994	9383	MARA	0/0	100.0	98.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00043	9398	9832	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00008	16349	17581	MDFA	0/0	100.0	98.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00023	20118	21365	MDTA	0/0	100.0	95.8	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00023	16996	20118	MDTB	0/0	100.0	95.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00023	13918	16995	MDTC	0/0	100.0	93.9	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00005	189615	190772	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00005	190797	193910	MDTF	0/0	100.0	97.3	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00011	69746	70972	MDTG	0/0	100.0	98.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00011	59907	61115	MDTH	0/0	100.0	98.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00006	136641	136970	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00006	136289	136654	MDTJ	0/0	100.0	97.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00006	54354	55726	MDTK	0/0	99.9	98.4	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00022	12407	13438	MDTN	0/0	100.0	94.9	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00022	10356	12407	MDTO	0/0	100.0	97.1	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00022	8893	10359	MDTP	0/0	100.0	97.7	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00099	68	989	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00008	95721	97469	MSBA	0/0	100.0	98.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00028	62521	62853	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00089	579	1409	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00012	122036	123937	PBP2	0/0	100.0	98.5	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00003	185233	186201	PMRF	0/0	100.0	97.7	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00013	41062	41931	ROBA	0/0	100.0	97.2	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00032	19176	19498	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00081	1707	2522	SULII	0/0	100.0	100.0	MEG_6618	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00093	516	1761	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00080	770	1975	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00080	2769	3185	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00023	75746	76912	UGD	0/0	100.0	97.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00003	125058	126701	YOGI	0/0	100.0	97.9	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID020at24

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00092	4914	5774	aac(3)-IId_1	0/0	100.0	99.9	EU022314	aac(3)-IId	Gentamicin, Tobramycin
contig00002	187467	188342	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00124	88	729	catA2_1	0/0	100.0	96.1	X53796	catA2	Chloramphenicol
contig00036	1689	2162	dfrA1_8	0/0	100.0	100.0	X00926	dfrA1	Trimethoprim
contig00128	614	1111	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00001	101828	103060	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00130	68	989	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00091	414	1280	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00094	2246	3037	sul3_2	0/0	100.0	100.0	AJ459418	sul3	Sulfamethoxazole
contig00101	2337	3583	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline
contig00126	158	1425	tet(K)_1	0/0	91.9	100.0	U38656	tet(K)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00092	4914	5774	AAC(3)-IId	0/0	100.0	99.9	EU022314.1:0-861	AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00011	41403	44552	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00017	22104	25217	acrD	0/0	100.0	99.3	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00047	8641	9798	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00047	5525	8629	acrF	0/0	100.0	100.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00047	10197	10859	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	89700	90521	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00046	31115	31837	baeR	0/0	100.0	99.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00046	29715	31118	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00124	88	729	catII_from_Escherichia_coli_K-12	0/0	100.0	96.1	X53796.1:186-828	catII is a chloramphenicol acetyltransferase. This particular catII is found in E.coli K-12. Confers resistance to chloramphenicol.	phenicol
contig00021	61537	62910	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00006	15387	16019	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00002	187467	188342	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00036	1689	2162	dfrA1	0/0	100.0	99.8	KJ541681.1:19526-20000	dfrA1 is an integron-encoded dihydrofolate reductase	diaminopyrimidine
contig00128	614	1111	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00088	427	1599	emrA	0/0	100.0	99.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00088	1616	3154	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00010	108528	109583	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00010	106990	108528	emrY	0/0	100.0	99.9	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00004	178263	179906	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00011	40187	41380	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	134908	136041	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00017	56548	57852	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.7	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00033	27471	28628	Escherichia_coli_ampH	0/0	100.0	99.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00001	101828	103060	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00041	377	991	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00041	996	4589	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00038	2242	2970	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00038	1051	1875	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00053	23647	24060	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00020	8002	8679	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00044	28957	29340	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00046	20855	22102	mdtA	0/0	100.0	98.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00046	22102	25224	mdtB	0/0	100.0	97.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00046	25225	28302	mdtC	0/0	100.0	97.7	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00038	6471	7628	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00038	3333	6446	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00019	17779	19005	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00019	27634	28842	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00014	28251	29483	mdtM	0/0	100.0	96.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00012	10896	11927	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00012	11927	13978	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00012	13975	15441	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00130	68	973	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00017	944	1420	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	184776	186524	msbA	0/0	100.0	99.9	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00010	8072	9040	pmrF	0/0	100.0	99.9	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00094	734	1066	qacH	0/0	100.0	91.6	DQ149925.1:188-521	qacH is a subunit of the qac multidrug efflux pump in Vibrio cholerae	fluoroquinolone
contig00036	2257	2781	SAT-1	0/0	100.0	100.0	AB211124:0-525	SAT-2 is a plasmid-mediated streptothricin acetyltransferase which confers resistance to streptothricin a nucleoside antibiotic. Originally described from an E. coli plasmid sequence by Heim et al. 1989.	nucleoside
contig00091	441	1280	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00094	2246	3037	sul3	0/0	100.0	100.0	FJ196385:9323-8531	Sul3 is a sulfonamide resistant dihydropteroate synthase similar to Sul1 and Sul2. Its resistance gene was found encoded in E. coli plasmid DNA of sulfonamide resistant isolates.	sulfonamide
contig00101	2337	3583	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00126	158	1425	tet(K)	0/0	91.9	100.0	S67449.1:0-1380	TetK is a tetracycline efflux protein found in both Gram-negative (Haemophilus and Gallibacterium) and Gram-positive (many species including mycobacteria) bacteria.	tetracycline
contig00005	65835	67322	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00025	50862	52505	yojI	0/0	100.0	99.9	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00092	4914	5774	(AGly)aac3-IId	0/0	100.0	99.9	EU022314:1-861	(AGly)aac3-IId	NA
contig00036	2828	3627	(AGly)aadA1-pm	1/3	96.3	99.5	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00036	2257	2781	(AGly)sat-2A	0/0	100.0	100.0	X51546:518-1042	(AGly)sat-2A	NA
contig00017	56548	57852	(Bla)AmpC1_Ecoli	0/0	100.0	98.7	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00004	134908	136041	(Bla)AmpC2_Ecoli	0/0	100.0	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00033	27471	28628	(Bla)ampH_Ecoli	0/0	100.0	99.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00002	187467	188342	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00020	60089	61990	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00130	68	973	(MLS)mph(A)	0/0	100.0	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00124	88	729	(Phe)catA2	0/0	100.0	96.1	X53796:187-903	(Phe)catA2	NA
contig00091	441	1280	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00094	2246	3037	(Sul)sul3	0/0	100.0	100.0	HQ875016:7396-8187	(Sul)sul3	NA
contig00101	2309	3583	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00126	158	1425	(Tet)tetK	0/0	91.9	100.0	M16217:305-1684	(Tet)tetK	NA
contig00101	3614	4264	(Tet)tetR	0/0	100.0	99.8	HF545434:53576-54226	(Tet)tetR	NA
contig00036	1689	2162	(Tmt)dfrA1	0/0	100.0	100.0	JQ794607:474	(Tmt)dfrA1	NA
contig00128	614	1111	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00092	4914	5774	aac(3)-IId	0/0	100.0	100.0	NG_047251.1	aminoglycoside N-acetyltransferase AAC(3)-IId	GENTAMICIN
contig00036	2839	3627	aadA1	0/0	100.0	100.0	NG_047327.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1	STREPTOMYCIN
contig00002	187467	188342	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00004	134908	136041	blaEC	0/0	100.0	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00124	88	729	catA2	0/0	100.0	100.0	NG_047596.1	type A-2 chloramphenicol O-acetyltransferase CatII	CHLORAMPHENICOL
contig00036	1689	2162	dfrA1	0/0	100.0	100.0	NG_047676.1	trimethoprim-resistant dihydrofolate reductase DfrA1	TRIMETHOPRIM
contig00128	614	1111	dfrA12	0/0	100.0	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00130	68	989	mph(A)	1/1	100.0	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00036	2257	2781	sat2_gen	0/0	100.0	100.0	NG_048068.1	streptothricin N-acetyltransferase Sat2	STREPTOTHRICIN
contig00091	441	1280	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00094	2246	3037	sul3	0/0	100.0	100.0	NG_048120.1	sulfonamide-resistant dihydropteroate synthase Sul3	SULFONAMIDE
contig00101	2309	3508	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE
contig00126	158	1425	tet(K)	0/0	91.9	100.0	NG_048200.1	tetracycline efflux MFS transporter Tet(K)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00092	4914	5774	AAC3	0/0	100.0	100.0	MEG_64	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00011	40187	41380	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00011	41403	44552	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00017	22104	25217	ACRD	0/0	100.0	99.3	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00047	8641	9798	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00047	5525	8629	ACRF	0/0	100.0	100.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00047	10197	10859	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00004	134908	136041	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00033	27471	28628	AMPH	0/0	100.0	99.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00036	2828	3627	ANT3-DPRIME	1/3	96.3	99.5	MEG_915	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00046	6739	8591	ASMA	0/0	100.0	97.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00005	89700	90521	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00046	31115	31837	BAER	0/0	100.0	99.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00046	29715	31118	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00015	67340	68530	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00124	88	729	CATA	0/0	100.0	100.0	MEG_1568	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00021	60842	61540	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00021	61537	62910	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00006	15387	16019	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00090	3505	4447	CTX	0/0	100.0	98.1	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00112	334	1222	CTX	0/0	100.0	95.4	MEG_2430	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00036	1689	2162	DFRA	0/0	100.0	99.8	MEG_2495	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00128	614	1111	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00088	427	1599	EMRA	0/0	100.0	99.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00088	1616	3154	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00008	87250	88440	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00010	108528	109686	EMRK	0/0	99.6	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00010	106990	108528	EMRY	0/0	100.0	99.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00004	178263	179906	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00041	996	4589	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00038	2242	2970	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00038	1051	1875	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00053	23647	24060	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00020	8002	8679	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00044	28951	29340	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00044	28503	28937	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00001	101828	103060	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00046	20855	22102	MDTA	0/0	100.0	98.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00046	22102	25224	MDTB	0/0	100.0	97.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00046	25225	28302	MDTC	0/0	100.0	97.7	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00038	6471	7628	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00038	3333	6446	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00019	17779	19005	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00019	27634	28842	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00042	632	961	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00042	948	1313	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00009	76121	77494	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00014	28251	29483	MDTM	0/0	100.0	96.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00012	10896	11927	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00012	11927	13978	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00012	13975	15441	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00130	68	989	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00017	944	1420	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	184776	186524	MSBA	0/0	100.0	99.9	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00020	60089	61990	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00017	56548	57852	PBP4B	0/0	100.0	98.7	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00010	8072	9040	PMRF	0/0	100.0	99.9	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00094	734	1066	QACL	0/0	100.0	100.0	MEG_5852	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACL	NA
contig00003	175115	175984	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00012	37058	37381	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00091	440	1407	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00094	2246	3037	SULIII	0/0	100.0	100.0	MEG_6639	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULIII	NA
contig00101	2309	3583	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00126	158	1425	TETK	0/0	91.9	100.0	MEG_7089	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETK	NA
contig00025	50862	52505	YOGI	0/0	100.0	99.9	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID021at24

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	1392	2180	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00078	498	1373	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00094	788	1261	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00002	154454	155686	mdf(A)_1	0/0	100	98.3	Y08743	mdf(A)
contig00094	8861	9782	mph(A)_2	1/1	100	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00078	6014	6670	qnrS1_1	0/0	100	100.0	AB187515	qnrS1	Ciprofloxacin
contig00094	2700	3566	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	1392	2180	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00001	103356	106505	acrB	0/0	100.0	99.5	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	71682	74795	acrD	0/0	100.0	98.9	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00058	8406	9563	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00058	5290	8394	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00058	9962	10624	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00019	28559	29380	bacA	0/0	100.0	99.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00002	50563	51285	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00002	49163	50566	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00035	37431	38804	cpxA	0/0	100.0	98.7	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00005	15464	16096	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00078	498	1373	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00094	788	1261	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00003	27410	28582	emrA	0/0	100.0	99.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00003	28599	30137	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00046	8783	9838	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00003	26753	27283	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00046	7245	8783	emrY	0/0	100.0	98.9	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00013	76745	78388	eptA	0/0	100.0	99.3	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00001	106528	107721	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00013	33384	34517	Escherichia_coli_ampC	0/0	100.0	97.6	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00006	106194	107498	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	96.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00001	17240	18397	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00002	154454	155686	Escherichia_coli_mdfA	0/0	100.0	96.8	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00046	10362	10976	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00046	10981	14574	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00042	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00042	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00025	5169	5582	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00007	23675	24352	kdpE	0/0	100.0	99.7	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00054	31308	31691	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00002	40303	41550	mdtA	0/0	100.0	99.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00002	41550	44672	mdtB	0/0	100.0	99.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00002	44673	47750	mdtC	0/0	100.0	99.8	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00042	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00042	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00004	124760	125986	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00004	114922	116130	mdtH	0/0	100.0	97.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00061	6012	7244	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00055	1	2040	mdtO	0/0	99.4	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00055	2037	3503	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00094	8877	9782	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00006	50468	50944	mphB	0/0	100.0	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00011	81416	83164	msbA	0/0	100.0	99.9	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00080	1339	2307	pmrF	0/0	100.0	99.8	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00078	6014	6670	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00094	2727	3566	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00087	5852	7339	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00023	56976	58619	yojI	0/0	100.0	99.3	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	1392	2180	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00006	106194	107498	(Bla)AmpC1_Ecoli	0/0	100	96.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00013	33384	34517	(Bla)AmpC2_Ecoli	0/0	100	97.6	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00001	17240	18397	(Bla)ampH_Ecoli	0/0	100	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00078	498	1373	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00007	76088	77989	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00078	6014	6670	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00094	8877	9782	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00094	2727	3566	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00094	788	1261	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	1392	2180	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00078	498	1373	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00013	33384	34517	blaEC-18	0/0	100	99.1	NG_049083.1	class C extended-spectrum beta-lactamase EC-18	CEPHALOSPORIN
contig00094	788	1261	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00094	8861	9782	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00078	6014	6670	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00094	2727	3566	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00001	106528	107721	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00001	103356	106505	ACRB	0/0	100.0	99.5	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00006	71682	74795	ACRD	0/0	100.0	98.9	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00058	8406	9563	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00058	5290	8394	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00058	9962	10624	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00001	17240	18397	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00094	1392	2180	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00002	26048	27900	ASMA	0/0	100.0	98.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00019	28559	29380	BACA	0/0	100.0	99.9	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00002	50563	51285	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00002	49163	50566	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00039	19164	20354	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00013	33384	34517	BLAEC	0/0	100.0	99.1	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00035	36736	37434	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00035	37431	38804	CPXAR	0/0	100.0	99.4	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00005	15464	16096	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00094	788	1261	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00003	27410	28582	EMRA	0/0	100.0	99.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00003	28599	30137	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00016	28895	30085	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00046	8783	9946	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00003	26753	27283	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00046	7245	8783	EMRY	0/0	100.0	99.0	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00013	76745	78388	EPTA	0/0	100.0	99.3	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00046	10981	14574	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00042	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00042	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00025	5169	5582	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00007	23675	24352	KDPE	0/0	100.0	99.7	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00054	31302	31691	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00054	30854	31288	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00002	154454	155686	MDFA	0/0	100.0	98.4	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00002	40303	41550	MDTA	0/0	100.0	99.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00002	41550	44672	MDTB	0/0	100.0	99.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00002	44673	47750	MDTC	0/0	100.0	99.8	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00042	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00042	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00004	124760	125986	MDTG	0/0	100.0	99.9	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00004	114922	116130	MDTH	0/0	100.0	97.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00010	80532	80861	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00010	80180	80545	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00010	8883	10256	MDTK	0/0	100.0	98.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00061	6012	7244	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00055	1	2040	MDTO	0/0	99.4	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00055	2037	3503	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00094	8861	9782	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00006	50468	50944	MPHB	0/0	100.0	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00011	81416	83164	MSBA	0/0	100.0	99.9	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00007	76088	77989	PBP2	0/0	100.0	99.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00006	106194	107498	PBP4B	0/0	100.0	96.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00080	1339	2307	PMRF	0/0	100.0	99.8	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00078	6014	6670	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00044	21726	22595	ROBA	0/0	100.0	98.8	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00055	25459	25781	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00094	2726	3693	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00023	56976	58619	YOGI	0/0	100.0	99.3	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID025III

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00114	1172	1973	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig02536	13	816	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00117	2038	2838	blaCTX-M-156_1	0/0	91.4	100.0	KM211509	blaCTX-M-156	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00114	2371	2868	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig01746	253	1013	erm(B)_18	2/2	99.6	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00055	865	2097	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig01661	68	998	mph(A)_2	2/10	100.0	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00962	11	826	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00114	1172	1951	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00367	1254	1916	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig02536	13	816	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00117	2038	2838	CTX-M-15	0/0	91.4	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00114	2371	2868	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00254	1	1481	eptA	0/0	90.1	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig01746	279	1013	ErmB	0/0	98.4	99.3	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00232	144	1277	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00055	865	2097	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig01603	277	954	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig02480	237	566	Klebsiella_pneumoniae_KpnF	0/0	100.0	100.0	AP006725.1:2484238-2484568	KpnF subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan.	aminoglycoside, cephalosporin, macrolide, peptide, rifamycin, tetracycline
contig00796	225	1455	mdtA	0/0	98.6	97.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00549	519	1697	mdtG	0/0	96.1	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00148	918	2384	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig01661	68	970	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00802	918	1394	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00962	11	826	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00114	1172	1951	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig02536	13	816	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00232	144	1277	(Bla)AmpC2_Ecoli	0/0	100.0	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00117	2038	2838	(Bla)blaCTX-M-15	0/0	91.4	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig01746	279	1013	(MLS)erm(B)	0/0	99.6	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig01661	68	970	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00962	11	826	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00114	2371	2868	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00114	1172	1963	aadA2	0/0	100.0	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig02536	13	822	aph(3’’)-Ib	0/0	97.8	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00117	2038	2838	blaCTX-M-15	0/0	91.4	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00232	144	1277	blaEC	0/0	100.0	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00114	2371	2868	dfrA12	0/0	100.0	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig01746	279	1013	erm(B)	0/0	99.6	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig01661	68	998	mph(A)	2/10	100.0	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00962	11	826	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00367	1254	1916	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00232	144	1277	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00114	1172	1973	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig02536	13	822	APH3-DPRIME	0/0	97.8	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00482	1	1665	ASMA	0/0	91.3	99.1	MEG_1179	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig03658	1	636	CPXAR	0/0	91.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00114	2371	2868	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00254	1	1481	EPTA	0/0	90.1	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig01746	253	1013	ERMB	2/2	99.6	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig01603	277	954	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig02480	237	566	KPNF	0/0	100.0	100.0	MEG_3515	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:KPNF	NA
contig00055	865	2097	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00796	225	1455	MDTA	0/0	98.6	97.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00549	519	1697	MDTG	0/0	96.1	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00148	918	2384	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig01661	68	998	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00802	918	1394	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00332	36	359	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00962	11	826	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA

ID025II

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00089	2721	3522	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00009	91518	92393	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00089	1826	2323	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00125	263	1026	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00008	30310	31542	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00089	10161	11091	mph(A)_2	2/10	100.0	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00089	4000	4866	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00118	850	2055	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00089	2743	3522	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00007	99712	102861	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00027	52378	55491	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00062	21524	22681	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00062	20463	21125	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	89049	89870	bacA	0/0	100.0	99.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00053	29821	30543	baeR	0/0	100.0	99.6	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00053	28421	29824	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00005	61439	62812	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00003	15201	15833	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00009	91518	92393	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00089	1826	2323	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00069	11909	13081	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00069	13098	14636	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00020	1067	2122	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00069	11252	11782	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00016	46590	48233	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00125	289	1034	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00007	98496	99689	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00017	13415	14548	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00020	65523	66827	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00012	64067	65224	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00008	30310	31542	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00020	2646	3260	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00020	3265	6858	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00042	2699	3427	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00042	1507	2331	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00059	24863	25276	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00024	8065	8742	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00053	19561	20808	mdtA	0/0	100.0	97.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00053	20808	23930	mdtB	0/0	100.0	99.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00053	23931	27008	mdtC	0/0	100.0	99.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00042	6928	8085	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00042	3790	6903	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00038	16626	17852	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00038	26481	27689	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00061	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00016	16021	17052	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00016	13970	16021	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00016	12507	13973	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00089	10189	11091	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00027	31216	31692	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00002	51374	53122	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00001	136290	137258	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00089	4027	4866	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00118	850	2055	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00006	65184	66671	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	76187	77830	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00089	2743	3522	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00020	65523	66827	(Bla)AmpC1_Ecoli	0/0	100.0	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00017	13415	14548	(Bla)AmpC2_Ecoli	0/0	100.0	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00012	64067	65224	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00009	91518	92393	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00024	60152	62053	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00125	289	1026	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00089	10189	11091	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00089	4027	4866	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00118	850	2055	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00089	1826	2323	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00089	2731	3522	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00009	91518	92393	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00017	13415	14548	blaEC	0/0	100	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00089	1826	2323	dfrA12	0/0	100	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00125	289	1026	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00089	10161	11091	mph(A)	2/10	100	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00089	4027	4866	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00118	850	2055	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00007	98496	99689	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00007	99712	102861	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00027	52378	55491	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00062	21524	22681	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00062	20463	21125	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00017	13415	14548	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00012	64067	65224	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00089	2721	3522	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00053	5770	7622	ASMA	0/0	100.0	97.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00006	89049	89870	BACA	0/0	100.0	99.9	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00053	29821	30543	BAER	0/0	100.0	99.6	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00053	28421	29824	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	49210	50400	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00005	60744	61442	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00005	61439	62812	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00003	15201	15833	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00146	62	1004	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00089	1826	2323	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00069	11909	13081	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00069	13098	14636	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00004	87171	88361	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00020	1067	2230	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00069	11252	11782	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00016	46590	48233	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00125	263	1026	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00020	3265	6858	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00042	2699	3427	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00042	1507	2331	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00059	24863	25276	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00024	8065	8742	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00056	30890	31324	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00008	30310	31542	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00053	19561	20808	MDTA	0/0	100.0	97.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00053	20808	23930	MDTB	0/0	100.0	99.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00053	23931	27008	MDTC	0/0	100.0	99.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00042	6928	8085	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00042	3790	6903	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00038	16626	17852	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00038	26481	27689	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00050	1757	2086	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00050	2073	2438	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00026	31960	33333	MDTK	0/0	100.0	98.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00061	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00016	16021	17052	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00016	13970	16021	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00016	12507	13973	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00089	10161	11091	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00027	31216	31692	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00002	51374	53122	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00024	60152	62053	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00020	65523	66827	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	136290	137258	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00063	4214	5083	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00025	9090	9413	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00089	4026	4993	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00118	850	2055	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00001	76187	77830	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID025I

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00074	2721	3522	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00023	6419	7294	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00074	1826	2323	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00103	263	1026	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00001	82540	83772	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00074	10161	11091	mph(A)_2	2/10	100.0	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00074	4000	4866	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00099	1132	2337	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00074	2743	3522	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00003	99712	102861	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00022	71642	74755	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00049	8641	9798	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00049	5525	8629	acrF	0/0	100.0	99.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00049	10197	10859	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	90602	91423	bacA	0/0	100.0	99.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00044	29821	30543	baeR	0/0	100.0	99.6	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00044	28421	29824	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00010	61323	62696	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00007	15201	15833	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00023	6419	7294	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00074	1826	2323	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00005	90366	91538	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00005	91555	93093	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00021	1067	2122	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00005	89709	90239	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00032	7757	9400	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00103	289	1034	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00003	98496	99689	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00011	40938	42071	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00021	65523	66827	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00003	187826	188983	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00001	82540	83772	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00021	2646	3260	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00021	3265	6858	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00040	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00040	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00033	47705	48118	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00025	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00045	31344	31727	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00044	19561	20808	mdtA	0/0	100.0	97.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00044	20808	23930	mdtB	0/0	100.0	99.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00044	23931	27008	mdtC	0/0	100.0	99.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00040	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00040	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00001	311993	313219	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00001	321848	323056	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00053	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00013	21757	22788	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00013	22788	24839	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00013	24836	26302	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00074	10189	11091	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00022	50480	50956	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	165487	167235	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00002	173705	174673	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00074	4027	4866	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00099	1132	2337	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00006	66737	68224	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00002	113602	115245	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00074	2743	3522	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00021	65523	66827	(Bla)AmpC1_Ecoli	0/0	100.0	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00011	40938	42071	(Bla)AmpC2_Ecoli	0/0	100.0	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00003	187826	188983	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00023	6419	7294	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00025	60155	62056	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00103	289	1026	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00074	10189	11091	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00074	4027	4866	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00099	1132	2337	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00074	1826	2323	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00074	2731	3522	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00023	6419	7294	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00011	40938	42071	blaEC	0/0	100	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00074	1826	2323	dfrA12	0/0	100	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00103	289	1026	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00074	10161	11091	mph(A)	2/10	100	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00074	4027	4866	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00099	1132	2337	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	98496	99689	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00003	99712	102861	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00022	71642	74755	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00049	8641	9798	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00049	5525	8629	ACRF	0/0	100.0	99.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00049	10197	10859	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00011	40938	42071	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00003	187826	188983	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00074	2721	3522	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00044	5770	7622	ASMA	0/0	100.0	97.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00006	90602	91423	BACA	0/0	100.0	99.9	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00044	29821	30543	BAER	0/0	100.0	99.6	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00044	28421	29824	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00002	86625	87815	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00010	60628	61326	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00010	61323	62696	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	15201	15833	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00121	62	1004	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00074	1826	2323	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00005	90366	91538	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00005	91555	93093	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00008	87171	88361	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00021	1067	2230	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00005	89709	90239	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00032	7757	9400	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00103	263	1026	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00021	3265	6858	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00040	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00040	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00033	47705	48118	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00025	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00045	31338	31727	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00045	30890	31324	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00001	82540	83772	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00044	19561	20808	MDTA	0/0	100.0	97.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00044	20808	23930	MDTB	0/0	100.0	99.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00044	23931	27008	MDTC	0/0	100.0	99.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00040	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00040	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00001	311993	313219	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00001	321848	323056	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00043	1757	2086	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00043	2073	2438	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00027	31963	33336	MDTK	0/0	100.0	98.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00053	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00013	21757	22788	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00013	22788	24839	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00013	24836	26302	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00074	10161	11091	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00022	50480	50956	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	165487	167235	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00025	60155	62056	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00021	65523	66827	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00002	173705	174673	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00004	19983	20852	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00013	47919	48242	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00074	4026	4993	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00099	1132	2337	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00002	113602	115245	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID026

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00073	2721	3522	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00014	91518	92393	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00073	1826	2323	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00099	263	1026	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00001	84130	85362	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00110	68	998	mph(A)_2	2/10	100.0	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00073	4000	4866	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00094	850	2055	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00073	2743	3522	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00002	39346	42495	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00023	71642	74755	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00008	127797	128954	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00008	128966	132070	acrF	0/0	100.0	99.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00008	126736	127398	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	90602	91423	bacA	0/0	100.0	99.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00048	29821	30543	baeR	0/0	100.0	99.6	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00048	28421	29824	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00011	61323	62696	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00007	15201	15833	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00014	91518	92393	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00073	1826	2323	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00006	90366	91538	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00006	91555	93093	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00022	1067	2122	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00006	89709	90239	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00034	1544	3187	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00099	289	1034	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00002	38130	39323	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	107745	108878	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00022	65523	66827	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00002	127460	128617	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00001	84130	85362	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00022	2646	3260	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00022	3265	6858	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00042	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00042	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00036	43265	43678	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00025	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00049	31344	31727	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00048	19561	20808	mdtA	0/0	100.0	97.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00048	20808	23930	mdtB	0/0	100.0	99.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00048	23931	27008	mdtC	0/0	100.0	99.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00042	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00042	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00035	19640	20866	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00035	29495	30703	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00055	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00016	10928	11959	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00016	11959	14010	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00016	14007	15473	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00110	68	970	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00023	50480	50956	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	167077	168825	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00003	136373	137341	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00073	4027	4866	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00094	850	2055	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00005	66737	68224	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00003	76270	77913	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00073	2743	3522	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00022	65523	66827	(Bla)AmpC1_Ecoli	0/0	100.0	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00004	107745	108878	(Bla)AmpC2_Ecoli	0/0	100.0	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00002	127460	128617	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00014	91518	92393	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00025	60155	62056	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00099	289	1026	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00110	68	970	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00073	4027	4866	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00094	850	2055	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00073	1826	2323	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00073	2731	3522	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00014	91518	92393	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00004	107745	108878	blaEC	0/0	100	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00073	1826	2323	dfrA12	0/0	100	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00099	289	1026	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00110	68	998	mph(A)	2/10	100	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00073	4027	4866	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00094	850	2055	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	38130	39323	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00002	39346	42495	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00023	71642	74755	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00008	127797	128954	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00008	128966	132070	ACRF	0/0	100.0	99.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00008	126736	127398	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00004	107745	108878	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00002	127460	128617	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00073	2721	3522	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00048	5770	7622	ASMA	0/0	100.0	97.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00005	90602	91423	BACA	0/0	100.0	99.9	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00048	29821	30543	BAER	0/0	100.0	99.6	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00048	28421	29824	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00003	49293	50483	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00011	60628	61326	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00011	61323	62696	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	15201	15833	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00116	61	984	CTX	0/0	98.0	98.3	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00073	1826	2323	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00006	90366	91538	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00006	91555	93093	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00009	87171	88361	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00022	1067	2230	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00006	89709	90239	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00034	1544	3187	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00099	263	1026	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00022	3265	6858	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00042	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00042	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00036	43265	43678	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00025	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00049	31338	31727	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00049	30890	31324	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00001	84130	85362	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00048	19561	20808	MDTA	0/0	100.0	97.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00048	20808	23930	MDTB	0/0	100.0	99.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00048	23931	27008	MDTC	0/0	100.0	99.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00042	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00042	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00035	19640	20866	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00035	29495	30703	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00046	1757	2086	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00046	2073	2438	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00026	31963	33336	MDTK	0/0	100.0	98.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00055	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00016	10928	11959	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00016	11959	14010	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00016	14007	15473	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00110	68	998	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00023	50480	50956	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	167077	168825	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00025	60155	62056	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00022	65523	66827	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00003	136373	137341	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00013	38665	39534	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00016	37090	37413	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00073	4026	4993	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00094	850	2055	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00003	76270	77913	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID027

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00079	2721	3522	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00034	6419	7294	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00079	1826	2323	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00102	263	1026	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00013	30137	31369	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00124	68	954	mph(A)_1	0/0	97.9	99.9	D16251	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00079	4000	4866	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00097	850	2055	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00079	2743	3522	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00010	98538	101687	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	135260	138373	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00051	8445	9602	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00051	5329	8433	acrF	0/0	100.0	99.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00051	10001	10663	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	90701	91522	bacA	0/0	100.0	99.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00047	29821	30543	baeR	0/0	100.0	99.6	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00047	28421	29824	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00009	61323	62696	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00007	15201	15833	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00034	6419	7294	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00079	1826	2323	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00014	19623	20795	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00014	20812	22350	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00024	1067	2122	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00014	18966	19496	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00003	120344	121987	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00102	289	1034	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00010	101710	102903	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00002	107745	108878	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00024	65523	66827	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00010	12416	13573	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00013	30137	31369	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00024	2646	3260	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00024	3265	6858	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00042	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00042	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00020	91674	92087	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00027	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00048	31519	31902	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00047	19561	20808	mdtA	0/0	100.0	97.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00047	20808	23930	mdtB	0/0	100.0	99.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00047	23931	27008	mdtC	0/0	100.0	99.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00042	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00042	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00035	16784	18010	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00035	26639	27847	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00058	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00003	89775	90806	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00003	87724	89775	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00003	86261	87727	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00124	68	954	mphA	0/0	97.9	99.9	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00006	114098	114574	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	125547	127295	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00004	62214	63182	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00079	4027	4866	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00097	850	2055	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00005	66836	68323	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00004	2111	3754	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00079	2743	3522	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00024	65523	66827	(Bla)AmpC1_Ecoli	0/0	100.0	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00002	107745	108878	(Bla)AmpC2_Ecoli	0/0	100.0	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00010	12416	13573	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00034	6419	7294	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00027	60155	62056	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00102	289	1026	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00124	68	954	(MLS)mph(A)	0/0	97.9	99.9	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00079	4027	4866	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00097	850	2055	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00079	1826	2323	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00079	2731	3522	aadA2	0/0	100.0	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00034	6419	7294	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00002	107745	108878	blaEC	0/0	100.0	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00079	1826	2323	dfrA12	0/0	100.0	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00102	289	1026	erm(B)	0/0	100.0	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00124	68	954	mph(A)	0/0	97.9	99.9	NG_047985.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00079	4027	4866	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00097	850	2055	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	101710	102903	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00010	98538	101687	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00006	135260	138373	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00051	8445	9602	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00051	5329	8433	ACRF	0/0	100.0	99.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00051	10001	10663	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00002	107745	108878	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00010	12416	13573	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00079	2721	3522	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00047	5770	7622	ASMA	0/0	100.0	97.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00005	90701	91522	BACA	0/0	100.0	99.9	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00047	29821	30543	BAER	0/0	100.0	99.6	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00047	28421	29824	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	23569	24759	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00009	60628	61326	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	61323	62696	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	15201	15833	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00123	62	988	CTX	0/0	98.3	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00079	1826	2323	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00014	19623	20795	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00014	20812	22350	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00008	87171	88361	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00024	1067	2230	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00014	18966	19496	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00003	120344	121987	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00102	263	1026	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00024	3265	6858	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00042	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00042	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00020	91674	92087	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00027	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00048	31513	31902	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00048	31065	31499	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00013	30137	31369	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00047	19561	20808	MDTA	0/0	100.0	97.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00047	20808	23930	MDTB	0/0	100.0	99.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00047	23931	27008	MDTC	0/0	100.0	99.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00042	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00042	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00035	16784	18010	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00035	26639	27847	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00017	103532	103861	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00017	103180	103545	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00017	31959	33332	MDTK	0/0	100.0	98.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00058	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00003	89775	90806	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00003	87724	89775	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00003	86261	87727	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00124	68	954	MPHA	0/0	97.9	99.9	MEG_4029	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00006	114098	114574	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	125547	127295	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00027	60155	62056	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00024	65523	66827	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00004	62214	63182	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00012	38665	39534	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00003	64321	64644	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00079	4026	4993	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00097	850	2055	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00004	2111	3754	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID031

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00079	1	834	aph(6)-Id_1	0/0	99.6	100.0	M28829	aph(6)-Id	Streptomycin
contig00031	2385	3260	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00087	73	555	dfrA14_5	0/0	100.0	99.8	DQ388123	dfrA14	Trimethoprim
contig00067	1489	2062	dfrA7_5	3/4	100.0	98.8	AJ419170	dfrA7	Trimethoprim
contig00006	5438	6670	mdf(A)_1	0/0	100.0	98.0	Y08743	mdf(A)
contig00067	179	1045	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00050	8201	9447	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00027	21643	24792	acrB	0/0	100.0	98.8	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	378940	382053	acrD	0/0	100.0	98.4	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00013	130114	131271	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00013	131283	134387	acrF	0/0	100.0	97.2	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00013	129053	129715	acrS	0/0	100.0	98.3	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00079	1	834	APH(6)-Id	0/0	99.6	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00003	237652	238471	bacA	0/0	99.8	98.2	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00034	25847	26568	baeR	0/0	99.9	97.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00034	24447	25850	baeS	0/0	100.0	90.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00023	29347	30720	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00009	15384	16016	CRP	0/0	100.0	99.0	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00031	2385	3260	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00087	73	555	dfrA14	0/0	100.0	100.0	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00067	1589	2062	dfrA7	0/0	100.0	100.0	FJ854362:2338-2812	dfrA7 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00010	36139	37311	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00010	37328	38866	emrB	0/0	100.0	97.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	285170	286225	emrK	0/0	100.0	97.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00010	35482	36012	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	283632	285170	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00025	3860	5503	eptA	0/0	100.0	91.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00027	24815	26008	Escherichia_coli_acrA	0/0	100.0	99.2	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00028	12860	13993	Escherichia_coli_ampC	0/0	100.0	97.5	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00004	225178	226335	Escherichia_coli_ampH	0/0	100.0	97.2	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00011	113754	114086	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00006	5438	6670	Escherichia_coli_mdfA	0/0	100.0	96.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	286749	287363	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	287368	290961	evgS	0/0	100.0	96.2	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00009	196304	197032	gadW	0/0	100.0	99.9	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00009	197401	198225	gadX	0/0	100.0	93.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00015	31236	31649	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00016	7188	7860	kdpE	0/0	99.3	95.8	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00026	22140	22523	marA	0/0	100.0	98.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00034	15587	16834	mdtA	0/0	100.0	95.8	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00034	16834	19956	mdtB	0/0	100.0	95.4	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00034	19957	23034	mdtC	0/0	100.0	92.3	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00009	191646	192803	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00009	192828	195941	mdtF	0/0	100.0	97.3	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00021	77335	78561	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00021	67496	68704	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00033	12206	13237	mdtN	0/0	100.0	95.1	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00033	10155	12206	mdtO	0/0	100.0	96.7	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00033	8692	10158	mdtP	0/0	100.0	97.6	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00006	130260	132008	msbA	0/0	100.0	98.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00001	185259	186227	pmrF	0/0	100.0	97.8	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00067	179	1018	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00050	8201	9447	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00003	210380	211867	tolC	0/0	100.0	98.2	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00020	40454	41620	ugd	0/0	100.0	96.1	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00001	125373	127016	yojI	0/0	100.0	98.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00079	1	834	(AGly)strB	0/0	99.6	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00028	12860	13993	(Bla)AmpC2_Ecoli	0/0	100.0	97.5	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00004	225178	226335	(Bla)ampH_Ecoli	0/0	100.0	97.2	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00031	2385	3260	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00016	60848	62749	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	98.6	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00067	179	1018	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00050	8173	9447	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00050	9478	10128	(Tet)tetR	0/0	100.0	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00087	73	546	(Tmt)dfrA14	0/0	100.0	99.8	GU726917:72-545	(Tmt)dfrA14	NA
contig00067	1589	2062	(Tmt)dhfr7	0/0	100.0	100.0	X58425:594-1067	(Tmt)dhfr7	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00079	1	834	aph(6)-Id	0/0	99.6	100	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00031	2385	3260	blaCTX-M-15	0/0	100.0	100	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00028	12860	13993	blaEC-19	0/0	100.0	99	NG_049084.1	class C extended-spectrum beta-lactamase EC-19	CEPHALOSPORIN
contig00087	73	546	dfrA14	0/0	100.0	100	NG_047696.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00067	1589	2062	dfrA7	0/0	100.0	100	NG_047737.1	trimethoprim-resistant dihydrofolate reductase DfrA7	TRIMETHOPRIM
contig00067	179	1018	sul1	0/0	100.0	100	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00050	8173	9372	tet(A)	0/0	100.0	100	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00027	24815	26008	ACRA	0/0	100.0	99.2	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00027	21643	24792	ACRB	0/0	100.0	98.8	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00001	378940	382053	ACRD	0/0	100.0	98.4	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00013	130114	131271	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00013	131283	134387	ACRF	0/0	100.0	97.2	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00013	129053	129715	ACRS	0/0	100.0	98.3	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00004	225178	226335	AMPH	0/0	100.0	97.2	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00079	1	834	APH6	0/0	99.6	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00034	2073	3925	ASMA	0/0	100.0	97.7	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00003	237652	238471	BACA	0/0	99.8	98.4	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00034	25847	26568	BAER	0/0	99.9	97.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00034	24447	25850	BAES	0/0	100.0	90.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	100550	101740	BCR	0/0	100.0	96.3	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00028	12860	13993	BLAEC	0/0	100.0	99.0	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00023	28652	29350	CPXAR	0/0	100.0	97.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00023	29347	30720	CPXAR	0/0	100.0	98.9	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	15384	16016	CRP	0/0	100.0	99.0	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00051	7643	8585	CTX	0/0	100.0	98.9	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00067	1589	2062	DFRA	0/0	100.0	100.0	MEG_2548	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00087	73	546	DFRA	0/0	100.0	100.0	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00010	36139	37311	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00010	37328	38866	EMRB	0/0	100.0	97.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00008	132845	134035	EMRD	0/0	100.0	98.1	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	285170	286333	EMRK	0/0	100.0	97.6	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00010	35482	36012	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	283632	285170	EMRY	0/0	100.0	97.8	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00025	3860	5503	EPTA	0/0	100.0	91.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	287368	290961	EVGS	0/0	100.0	97.3	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00009	196304	197032	GADW	0/0	100.0	99.9	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00009	197401	198225	GADX	0/0	100.0	93.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00015	31236	31649	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00016	7188	7860	KDPE	0/0	99.3	95.8	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00026	22134	22523	MARA	0/0	100.0	98.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00026	21685	22119	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00006	5438	6670	MDFA	0/0	100.0	98.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00034	15587	16834	MDTA	0/0	100.0	95.8	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00034	16834	19956	MDTB	0/0	100.0	95.4	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00034	19957	23034	MDTC	0/0	100.0	92.3	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00009	191646	192803	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00009	192828	195941	MDTF	0/0	100.0	97.3	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00021	77335	78561	MDTG	0/0	100.0	98.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00021	67496	68704	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00026	60188	60517	MDTI	0/0	100.0	98.5	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00026	60504	60869	MDTJ	0/0	100.0	98.4	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00005	36829	38202	MDTK	0/0	100.0	97.9	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00033	12206	13237	MDTN	0/0	100.0	95.1	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00033	10155	12206	MDTO	0/0	100.0	96.7	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00033	8692	10158	MDTP	0/0	100.0	97.6	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00006	130260	132008	MSBA	0/0	100.0	98.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00011	113754	114086	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00016	60848	62749	PBP2	0/0	100.0	98.6	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	185259	186227	PMRF	0/0	100.0	97.8	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00002	119196	120065	ROBA	0/0	100.0	97.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00022	19233	19555	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00067	52	1019	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00050	8173	9447	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00020	40454	41620	UGD	0/0	100.0	96.1	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00001	125373	127016	YOGI	0/0	100.0	98.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID032I

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00073	1696	2556	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00076	1540	2139	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00057	1303	2091	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00050	8895	9698	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00050	8059	8895	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00002	201260	202135	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00076	579	1409	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00057	699	1172	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00017	29907	31139	mdf(A)_1	0/0	100.0	97.8	Y08743	mdf(A)
contig00081	69	990	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00057	2611	3477	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00050	9759	10574	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00050	5810	7056	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00073	1696	2556	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00076	1540	2139	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00057	1303	2091	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00001	65991	69140	acrB	0/0	100.0	98.8	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	99480	102593	acrD	0/0	100.0	98.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00012	149292	150449	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00012	150461	153565	acrF	0/0	100.0	96.6	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00012	148231	148893	acrS	0/0	100.0	98.3	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00050	8895	9698	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00050	8059	8895	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00007	52237	53056	bacA	0/0	99.8	98.3	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00013	61611	62332	baeR	0/0	99.9	97.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00013	62329	63732	baeS	0/0	100.0	90.5	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00018	66690	68057	cpxA	0/0	99.6	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00008	15089	15721	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00002	201260	202135	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00057	699	1172	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00029	60267	61439	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00029	61456	62994	emrB	0/0	100.0	98.4	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00005	5710	6765	emrK	0/0	100.0	97.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00029	59610	60140	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00005	4172	5710	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00009	146400	148043	eptA	0/0	100.0	91.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00001	64775	65968	Escherichia_coli_acrA	0/0	100.0	99.1	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00032	30615	31748	Escherichia_coli_ampC	0/0	100.0	97.8	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	153890	155047	Escherichia_coli_ampH	0/0	100.0	97.1	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00014	28735	29067	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00017	29907	31139	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00005	7289	7903	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00005	7908	11501	evgS	0/0	100.0	96.3	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00008	188688	189416	gadW	0/0	100.0	100.0	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00008	189785	190609	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00025	39538	39951	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00006	53994	54666	kdpE	0/0	99.3	95.5	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00026	29733	30116	marA	0/0	100.0	99.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00013	71345	72592	mdtA	0/0	100.0	95.6	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00013	68223	71345	mdtB	0/0	100.0	96.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00013	65145	68222	mdtC	0/0	100.0	94.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00008	184030	185187	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00008	185212	188325	mdtF	0/0	100.0	97.3	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00011	91920	93146	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00011	82083	83291	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00031	38742	39974	mdtM	0/0	100.0	95.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00009	116127	117158	mdtN	0/0	100.0	96.2	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00009	114076	116127	mdtO	0/0	100.0	97.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00009	112613	114079	mdtP	0/0	100.0	97.6	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00081	69	974	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00023	5695	7443	msbA	0/0	100.0	98.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00076	579	1409	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00004	171344	172312	pmrF	0/0	100.0	97.6	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00057	2638	3477	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00050	9759	10574	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00050	5810	7056	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00007	78739	80226	tolC	0/0	100.0	98.2	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00013	125688	126854	ugd	0/0	100.0	96.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00004	111496	113139	yojI	0/0	100.0	97.4	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00073	1696	2556	(AGly)aac3-IIa	0/0	100	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00057	1303	2091	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00050	8895	9698	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00050	8059	8895	(AGly)strB	0/0	100	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00032	30615	31748	(Bla)AmpC2_Ecoli	0/0	100	97.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00001	153890	155047	(Bla)ampH_Ecoli	0/0	100	97.1	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00002	201260	202135	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00076	579	1409	(Bla)blaOXA-1	0/0	100	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00006	113211	115112	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00081	69	974	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00057	2638	3477	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00050	9759	10574	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00050	5782	7056	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00050	7087	7737	(Tet)tetR	0/0	100	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00057	699	1172	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00073	1696	2556	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00076	1540	2094	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00057	1303	2091	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00050	8895	9722	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00050	8059	8895	aph(6)-Id	0/0	100	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00002	201260	202135	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00032	30615	31748	blaEC-5	0/0	100	99.5	NG_049085.1	cephalosporin-hydrolyzing class C beta-lactamase EC-5	CEPHALOSPORIN
contig00076	579	1409	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00057	699	1172	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00081	69	990	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00057	2638	3477	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00050	9759	10574	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00050	5782	6981	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00073	1696	2556	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00001	64775	65968	ACRA	0/0	100.0	99.1	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00001	65991	69140	ACRB	0/0	100.0	98.8	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00005	99480	102593	ACRD	0/0	100.0	98.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00012	149292	150449	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00012	150461	153565	ACRF	0/0	100.0	96.6	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00012	148231	148893	ACRS	0/0	100.0	98.3	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00001	153890	155047	AMPH	0/0	100.0	97.1	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00057	1303	2091	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00050	8895	9722	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00050	8059	8895	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00013	84252	86104	ASMA	0/0	100.0	97.6	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00007	52237	53056	BACA	0/0	99.8	98.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00013	61611	62332	BAER	0/0	99.9	97.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00013	62329	63732	BAES	0/0	100.0	90.5	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00004	86673	87863	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00032	30615	31748	BLAEC	0/0	100.0	99.5	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00018	65995	66693	CPXAR	0/0	100.0	98.1	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00018	66690	68057	CPXAR	0/0	99.6	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00008	15089	15721	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00057	699	1172	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00029	60267	61439	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00029	61456	62994	EMRB	0/0	100.0	98.4	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00002	194231	195421	EMRD	0/0	100.0	97.5	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00005	5710	6873	EMRK	0/0	100.0	97.4	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00029	59610	60140	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00005	4172	5710	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00009	146400	148043	EPTA	0/0	100.0	91.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00005	7908	11501	EVGS	0/0	100.0	97.4	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00008	188688	189416	GADW	0/0	100.0	100.0	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00008	189785	190609	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00025	39538	39951	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00006	53994	54666	KDPE	0/0	99.3	95.5	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00026	29727	30116	MARA	0/0	100.0	99.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00026	29278	29712	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00017	29907	31139	MDFA	0/0	100.0	97.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00013	71345	72592	MDTA	0/0	100.0	95.6	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00013	68223	71345	MDTB	0/0	100.0	96.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00013	65145	68222	MDTC	0/0	100.0	94.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00008	184030	185187	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00008	185212	188325	MDTF	0/0	100.0	97.3	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00011	91920	93146	MDTG	0/0	100.0	98.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00011	82083	83291	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00026	60681	61010	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00026	60997	61362	MDTJ	0/0	100.0	98.4	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00021	60316	61688	MDTK	0/0	99.9	97.7	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00031	38742	39974	MDTM	0/0	100.0	95.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00009	116127	117158	MDTN	0/0	100.0	96.2	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00009	114076	116127	MDTO	0/0	100.0	97.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00009	112613	114079	MDTP	0/0	100.0	97.6	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00081	69	990	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00023	5695	7443	MSBA	0/0	100.0	98.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00014	28735	29067	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00076	579	1409	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00006	113211	115112	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00004	171344	172312	PMRF	0/0	100.0	97.6	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00003	19703	20572	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00009	84260	84582	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00057	2637	3604	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00050	9759	10574	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00050	5782	7056	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00013	125688	126854	UGD	0/0	100.0	96.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00004	111496	113139	YOGI	0/0	100.0	97.4	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID033I

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00060	19123	19926	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00060	18287	19123	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00060	15299	16174	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00096	183	665	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00048	27861	29093	mdf(A)_1	0/0	100.0	99.0	Y08743	mdf(A)
contig00060	10002	10658	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00060	19987	20802	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00091	1676	2922	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00040	38756	41905	acrB	0/0	100.0	99.5	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00012	71770	74883	acrD	0/0	100.0	99.3	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00003	144696	145853	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	145865	148969	acrF	0/0	100.0	99.1	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	143635	144297	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00060	19123	19926	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00060	18287	19123	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00016	65363	66184	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00008	91520	92242	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00008	90120	91523	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00014	61321	62694	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00004	14925	15557	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00060	15299	16174	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00096	183	665	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00053	28123	29295	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00053	29312	30850	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00050	3675	4730	emrK	0/0	100.0	99.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00053	27466	27996	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00050	2137	3675	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00026	7717	9360	eptA	0/0	100.0	99.5	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00040	37540	38733	Escherichia_coli_acrA	0/0	100.0	99.5	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00026	51573	52706	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00045	14217	15521	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.7	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00009	17331	18488	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00048	27861	29093	Escherichia_coli_mdfA	0/0	100.0	97.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00050	5254	5868	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00050	5873	9466	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00042	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00042	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00007	118839	119252	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00039	8002	8679	kdpE	0/0	100.0	99.4	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00017	46177	46560	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00008	81260	82507	mdtA	0/0	100.0	100.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00008	82507	85629	mdtB	0/0	100.0	98.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00008	85630	88707	mdtC	0/0	100.0	99.8	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00042	6013	7170	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00042	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00049	24804	26030	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00049	14968	16176	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00056	8672	9883	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00010	89191	90222	mdtN	0/0	100.0	99.5	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00010	87140	89191	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00010	85677	87143	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00012	50610	51086	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00006	2197	3945	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00002	62175	63143	pmrF	0/0	100.0	99.9	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00060	10002	10658	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00060	19987	20802	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00091	1676	2922	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00016	41500	42987	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00002	2050	3693	yojI	0/0	100.0	99.9	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00060	19123	19926	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00060	18287	19123	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00045	14217	15521	(Bla)AmpC1_Ecoli	0/0	100	98.7	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00026	51573	52706	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00009	17331	18488	(Bla)ampH_Ecoli	0/0	100	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00060	15299	16174	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00067	8261	10162	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00060	10002	10658	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00060	19987	20802	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00091	1648	2922	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00096	183	656	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00060	19123	19950	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00060	18287	19123	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00060	15299	16174	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00026	51573	52706	blaEC	0/0	100	98.2	NG_047496.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00096	183	656	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00060	10002	10658	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00060	19987	20802	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00091	1648	2847	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00040	37540	38733	ACRA	0/0	100.0	99.5	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00040	38756	41905	ACRB	0/0	100.0	99.5	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00012	71770	74883	ACRD	0/0	100.0	99.3	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00003	144696	145853	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00003	145865	148969	ACRF	0/0	100.0	99.1	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00003	143635	144297	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00009	17331	18488	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00060	19123	19950	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00060	18287	19123	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00008	66995	68847	ASMA	0/0	100.0	98.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00016	65363	66184	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00008	91520	92242	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00008	90120	91523	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00021	49342	50532	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00026	51573	52706	BLAEC	0/0	100.0	98.2	MEG_1276	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00014	60626	61324	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00014	61321	62694	CPXAR	0/0	100.0	99.4	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00004	14925	15557	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00076	132	1074	CTX	0/0	100.0	99.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00096	183	656	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00053	28123	29295	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00053	29312	30850	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00027	16748	17938	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00050	3675	4838	EMRK	0/0	100.0	99.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00053	27466	27996	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00050	2137	3675	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00026	7717	9360	EPTA	0/0	100.0	99.5	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00050	5873	9466	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00042	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00042	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00007	118839	119252	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00039	8002	8679	KDPE	0/0	100.0	99.4	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00017	46171	46560	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00017	45723	46157	MARR	0/0	100.0	99.8	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00048	27861	29093	MDFA	0/0	100.0	99.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00008	81260	82507	MDTA	0/0	100.0	100.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00008	82507	85629	MDTB	0/0	100.0	98.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00008	85630	88707	MDTC	0/0	100.0	99.8	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00042	6013	7170	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00042	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00049	24804	26030	MDTG	0/0	100.0	99.9	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00049	14968	16176	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00001	210422	210751	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00001	210070	210435	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00001	138668	140041	MDTK	0/0	100.0	98.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00056	8672	9883	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00010	89191	90222	MDTN	0/0	100.0	99.5	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00010	87140	89191	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00010	85677	87143	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00012	50610	51086	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00006	2197	3945	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00067	8261	10162	PBP2	0/0	100.0	99.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00045	14217	15521	PBP4B	0/0	100.0	98.7	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00002	62175	63143	PMRF	0/0	100.0	99.9	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00060	10002	10658	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00029	38115	38984	ROBA	0/0	100.0	98.8	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00010	63398	63720	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00060	19987	20802	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00091	1648	2922	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00002	2050	3693	YOGI	0/0	100.0	99.9	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID034II

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	2721	3522	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00080	6419	7294	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00070	1826	2323	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00101	263	1026	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00015	30313	31545	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00112	68	998	mph(A)_2	2/10	100.0	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00070	4000	4866	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00098	1132	2337	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	2743	3522	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00002	99712	102861	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00032	38918	42031	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00010	127797	128954	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00010	128966	132070	acrF	0/0	100.0	99.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00010	126736	127398	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	90602	91423	bacA	0/0	100.0	99.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00043	29821	30543	baeR	0/0	100.0	99.6	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00043	28421	29824	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00013	61200	62573	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00009	15201	15833	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00080	6419	7294	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00070	1826	2323	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00005	90366	91538	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00005	91555	93093	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00023	1067	2122	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00005	89709	90239	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00007	120014	121657	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00101	289	1034	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00002	98496	99689	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	107745	108878	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00023	65523	66827	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00002	187826	188983	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00015	30313	31545	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00023	2646	3260	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00023	3265	6858	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00038	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00038	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00018	91674	92087	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00076	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00044	31343	31726	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00043	19561	20808	mdtA	0/0	100.0	97.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00043	20808	23930	mdtB	0/0	100.0	99.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00043	23931	27008	mdtC	0/0	100.0	99.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00038	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00038	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00034	18401	19627	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00034	28256	29464	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00051	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00007	89445	90476	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00007	87394	89445	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00007	85931	87397	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00112	68	970	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00032	17756	18232	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00006	51374	53122	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00001	173705	174673	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00070	4027	4866	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00098	1132	2337	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00008	66737	68224	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	113602	115245	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	2743	3522	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00023	65523	66827	(Bla)AmpC1_Ecoli	0/0	100.0	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00004	107745	108878	(Bla)AmpC2_Ecoli	0/0	100.0	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00002	187826	188983	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00080	6419	7294	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00026	51171	53072	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00101	289	1026	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00112	68	970	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00070	4027	4866	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00098	1132	2337	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00070	1826	2323	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	2731	3522	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00080	6419	7294	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00004	107745	108878	blaEC	0/0	100	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00070	1826	2323	dfrA12	0/0	100	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00101	289	1026	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00112	68	998	mph(A)	2/10	100	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00070	4027	4866	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00098	1132	2337	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	98496	99689	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00002	99712	102861	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00032	38918	42031	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00010	127797	128954	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00010	128966	132070	ACRF	0/0	100.0	99.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00010	126736	127398	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00004	107745	108878	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00002	187826	188983	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00070	2721	3522	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00043	5770	7622	ASMA	0/0	100.0	97.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00008	90602	91423	BACA	0/0	100.0	99.9	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00043	29821	30543	BAER	0/0	100.0	99.6	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00043	28421	29824	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	86625	87815	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00013	60505	61203	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00013	61200	62573	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	15201	15833	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00120	62	1004	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00070	1826	2323	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00005	90366	91538	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00005	91555	93093	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00011	87171	88361	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00023	1067	2230	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00005	89709	90239	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00007	120014	121657	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00101	263	1026	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00023	3265	6858	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00038	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00038	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00018	91674	92087	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00076	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00044	31337	31726	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00044	30889	31323	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00015	30313	31545	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00043	19561	20808	MDTA	0/0	100.0	97.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00043	20808	23930	MDTB	0/0	100.0	99.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00043	23931	27008	MDTC	0/0	100.0	99.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00038	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00038	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00034	18401	19627	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00034	28256	29464	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00042	1757	2086	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00042	2073	2438	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00037	31963	33336	MDTK	0/0	100.0	98.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00051	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00007	89445	90476	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00007	87394	89445	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00007	85931	87397	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00112	68	998	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00032	17756	18232	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00006	51374	53122	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00026	51171	53072	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00023	65523	66827	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	173705	174673	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00003	28156	29025	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00007	63991	64314	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00070	4026	4993	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00098	1132	2337	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00001	113602	115245	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID034I

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00079	2721	3522	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00042	6419	7294	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00079	1826	2323	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00109	263	1026	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00007	67552	68784	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00120	68	998	mph(A)_2	2/10	100.0	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00079	4000	4866	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00103	850	2055	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00079	2743	3522	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00001	39392	42541	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	135351	138464	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00011	127888	129045	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00011	129057	132161	acrF	0/0	100.0	99.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00011	126827	127489	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00010	90602	91423	bacA	0/0	100.0	99.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00047	29821	30543	baeR	0/0	100.0	99.6	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00047	28421	29824	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00013	61323	62696	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00009	15750	16382	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00042	6419	7294	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00079	1826	2323	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00004	90366	91538	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00004	91555	93093	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00021	1067	2122	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00004	89709	90239	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00031	7767	9410	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00109	289	1034	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00001	38176	39369	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	107745	108878	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00021	65523	66827	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00001	127506	128663	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00007	67552	68784	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00021	2646	3260	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00021	3265	6858	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00065	2243	2971	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00065	1051	1875	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00017	91674	92087	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00057	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00048	31344	31727	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00047	19561	20808	mdtA	0/0	100.0	97.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00047	20808	23930	mdtB	0/0	100.0	99.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00047	23931	27008	mdtC	0/0	100.0	99.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00065	6472	7629	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00065	3334	6447	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00033	18401	19627	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00033	28256	29464	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00053	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00037	22336	23367	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00037	20285	22336	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00037	18822	20288	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00120	68	970	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00008	114189	114665	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00005	51374	53122	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00006	62062	63030	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00079	4027	4866	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00103	850	2055	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00010	66737	68224	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00006	1959	3602	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00079	2743	3522	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00021	65523	66827	(Bla)AmpC1_Ecoli	0/0	100.0	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00003	107745	108878	(Bla)AmpC2_Ecoli	0/0	100.0	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00001	127506	128663	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00042	6419	7294	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00032	38461	40362	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00109	289	1026	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00120	68	970	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00079	4027	4866	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00103	850	2055	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00079	1826	2323	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00079	2731	3522	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00042	6419	7294	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00003	107745	108878	blaEC	0/0	100	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00079	1826	2323	dfrA12	0/0	100	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00109	289	1026	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00120	68	998	mph(A)	2/10	100	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00079	4027	4866	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00103	850	2055	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00001	38176	39369	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00001	39392	42541	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00008	135351	138464	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00011	127888	129045	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00011	129057	132161	ACRF	0/0	100.0	99.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00011	126827	127489	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00003	107745	108878	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00001	127506	128663	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00079	2721	3522	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00047	5770	7622	ASMA	0/0	100.0	97.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00010	90602	91423	BACA	0/0	100.0	99.9	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00047	29821	30543	BAER	0/0	100.0	99.6	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00047	28421	29824	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00024	49210	50400	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00013	60628	61326	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00013	61323	62696	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	15750	16382	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00128	61	984	CTX	0/0	98.0	98.3	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00079	1826	2323	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00004	90366	91538	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00004	91555	93093	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00012	43177	44367	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00021	1067	2230	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00004	89709	90239	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00031	7767	9410	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00109	263	1026	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00021	3265	6858	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00065	2243	2971	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00065	1051	1875	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00017	91674	92087	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00057	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00048	31338	31727	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00048	30890	31324	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00007	67552	68784	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00047	19561	20808	MDTA	0/0	100.0	97.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00047	20808	23930	MDTB	0/0	100.0	99.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00047	23931	27008	MDTC	0/0	100.0	99.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00065	6472	7629	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00065	3334	6447	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00033	18401	19627	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00033	28256	29464	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00045	1757	2086	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00045	2073	2438	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00025	31963	33336	MDTK	0/0	100.0	98.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00053	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00037	22336	23367	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00037	20285	22336	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00037	18822	20288	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00120	68	998	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00008	114189	114665	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00005	51374	53122	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00032	38461	40362	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00021	65523	66827	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00006	62062	63030	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00002	19983	20852	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00026	2753	3076	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00079	4026	4993	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00103	850	2055	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00006	1959	3602	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID037

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00117	2601	3461	blaSHV-12_1	0/0	100	100.0	KF976405	blaSHV-12	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00072	18824	19306	dfrA14_5	0/0	100	99.6	DQ388123	dfrA14	Trimethoprim
contig00040	30290	31522	mdf(A)_1	0/0	100	99.9	Y08743	mdf(A)

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00022	35950	39099	acrB	0/0	100.0	99.8	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	134904	138017	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00057	8641	9798	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00057	5525	8629	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00057	10197	10859	acrS	0/0	100.0	99.1	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00002	95858	96679	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00001	132646	133368	baeR	0/0	100.0	98.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00001	133365	134768	baeS	0/0	100.0	98.8	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00020	22373	23746	cpxA	0/0	100.0	98.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00009	15387	16019	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00072	18824	19306	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00005	62310	63482	emrA	0/0	100.0	99.8	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00005	63499	65037	emrB	0/0	100.0	99.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00004	125401	126456	emrK	0/0	100.0	99.3	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00005	61653	62183	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00004	123863	125401	emrY	0/0	100.0	98.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00053	7690	9333	eptA	0/0	100.0	99.8	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00022	39122	40315	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00055	16878	18011	Escherichia_coli_ampC	0/0	100.0	98.5	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00003	169461	170765	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	97.8	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00024	49342	50499	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00040	30290	31522	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00004	126980	127594	evgA	0/0	100.0	99.3	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00004	127599	131192	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00037	40035	40763	gadW	0/0	100.0	94.5	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00037	41131	41955	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00027	5179	5592	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00099	8068	8745	kdpE	0/0	100.0	99.1	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00015	19337	19720	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00001	142381	143628	mdtA	0/0	100.0	99.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00001	139259	142381	mdtB	0/0	100.0	99.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00001	136181	139258	mdtC	0/0	100.0	99.5	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00037	35377	36534	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00037	36559	39672	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00008	84610	85836	mdtG	0/0	100.0	99.8	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00008	74771	75979	mdtH	0/0	100.0	97.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00071	262	1473	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00039	20077	21108	mdtN	0/0	100.0	99.9	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00039	18026	20077	mdtO	0/0	100.0	99.8	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00039	16563	18029	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00003	113964	114440	mphB	0/0	100.0	99.4	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00006	51524	53272	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00007	106948	107916	pmrF	0/0	100.0	99.6	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00117	2601	3461	SHV-134	0/0	100.0	99.9	HM559945:0-861	SHV-134 is an extended-spectrum beta-lactamase.	carbapenem, cephalosporin, penam
contig00002	71958	73445	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	194385	195551	ugd	0/0	100.0	96.2	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00007	47104	48747	yojI	0/0	100.0	99.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	169461	170765	(Bla)AmpC1_Ecoli	0/0	100	97.8	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00055	16878	18011	(Bla)AmpC2_Ecoli	0/0	100	98.5	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00024	49342	50499	(Bla)ampH_Ecoli	0/0	100	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00117	2601	3461	(Bla)blaSHV-12	0/0	100	100.0	FJ685654:24-860	(Bla)blaSHV-12	NA
contig00014	19999	21900	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.5	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00072	18824	19297	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00055	16878	18011	blaEC	0/0	100	100	NG_047496.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00117	2601	3461	blaSHV-12	0/0	100	100	NG_050590.1	class A extended-spectrum beta-lactamase SHV-12	CEPHALOSPORIN
contig00072	18824	19297	dfrA14	0/0	100	100	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00022	39122	40315	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00022	35950	39099	ACRB	0/0	100.0	99.8	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00003	134904	138017	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00057	8641	9798	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00057	5525	8629	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00057	10197	10859	ACRS	0/0	100.0	99.1	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00024	49342	50499	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00001	155297	157149	ASMA	0/0	100.0	93.8	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00002	95858	96679	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00001	132646	133368	BAER	0/0	100.0	98.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00001	133365	134768	BAES	0/0	100.0	98.8	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	8223	9413	BCR	0/0	100.0	97.1	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00055	16878	18011	BLAEC	0/0	100.0	100.0	MEG_1276	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00020	21678	22376	CPXAR	0/0	100.0	99.7	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00020	22373	23746	CPXAR	0/0	100.0	98.6	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	15387	16019	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00015	65608	66550	CTX	0/0	100.0	98.8	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00072	18824	19297	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00005	62310	63482	EMRA	0/0	100.0	99.8	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00005	63499	65037	EMRB	0/0	100.0	99.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00018	16827	18017	EMRD	0/0	100.0	99.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00004	125401	126564	EMRK	0/0	100.0	99.1	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00005	61653	62183	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00004	123863	125401	EMRY	0/0	100.0	98.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00053	7690	9333	EPTA	0/0	100.0	99.8	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00004	127599	131192	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00037	40035	40763	GADW	0/0	100.0	99.9	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00037	41131	41955	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00027	5179	5592	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00099	8068	8745	KDPE	0/0	100.0	99.1	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00015	19337	19726	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00015	19740	20174	MARR	0/0	100.0	97.5	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00040	30290	31522	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00001	142381	143628	MDTA	0/0	100.0	99.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00001	139259	142381	MDTB	0/0	100.0	99.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00001	136181	139258	MDTC	0/0	100.0	99.5	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00037	35377	36534	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00037	36559	39672	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00008	84610	85836	MDTG	0/0	100.0	99.8	MEG_3754	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00008	74771	75979	MDTH	0/0	100.0	97.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00048	309	638	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00023	12649	14022	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00071	262	1473	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00039	20077	21108	MDTN	0/0	100.0	99.9	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00039	18026	20077	MDTO	0/0	100.0	99.8	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00039	16563	18029	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00003	113964	114440	MPHB	0/0	100.0	99.4	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00006	51524	53272	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00014	19999	21900	PBP2	0/0	100.0	99.5	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00003	169461	170765	PBP4B	0/0	100.0	97.8	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00007	106948	107916	PMRF	0/0	100.0	99.6	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00060	10835	11704	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00117	2504	3507	SHV	0/0	99.7	98.9	MEG_6428	Drugs:betalactams:Class_A_betalactamases:SHV	NA
contig00104	1347	1670	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00001	194385	195551	UGD	0/0	100.0	96.2	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00007	47104	48747	YOGI	0/0	100.0	99.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID043I

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00080	35	895	aac(3)-IId_1	0/0	100.0	99.9	EU022314	aac(3)-IId	Gentamicin, Tobramycin
contig00072	3038	3826	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00081	1610	2412	aph(3’’)-Ib_2	0/0	99.9	100.0	AF024602	aph(3’’)-Ib	Streptomycin
contig00081	774	1610	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00032	28202	29077	blaCTX-M-14_1	0/0	100.0	100.0	AF252622	blaCTX-M-14	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00082	1835	2695	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00072	3957	4430	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00014	32368	33600	mdf(A)_1	0/0	100.0	98.1	Y08743	mdf(A)
contig00095	69	990	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00072	1652	2518	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00078	704	1519	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00080	35	895	AAC(3)-IId	0/0	100.0	99.9	EU022314.1:0-861	AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00072	3038	3826	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00043	12982	16131	acrB	0/0	100.0	99.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	134559	137672	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00017	83805	84962	acrE	0/0	100.0	98.4	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00017	84974	88078	acrF	0/0	100.0	97.8	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00017	82744	83406	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00081	1610	2413	APH(3’’)-Ib	0/0	100.0	99.9	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00081	774	1610	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00002	115744	116563	bacA	0/0	99.8	96.2	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00025	10839	11560	baeR	0/0	99.9	98.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00025	9439	10842	baeS	0/0	100.0	96.4	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00018	22716	24089	cpxA	0/0	100.0	98.6	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00009	15391	16023	CRP	0/0	100.0	99.0	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00032	28202	29077	CTX-M-14	0/0	100.0	100.0	AF252622:1740-2616	CTX-M-14 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00072	3957	4430	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00026	16391	17563	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00026	17580	19118	emrB	0/0	100.0	98.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00012	85378	86433	emrK	0/0	100.0	97.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00026	15734	16264	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00012	83840	85378	emrY	0/0	100.0	97.4	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00004	80809	82452	eptA	0/0	100.0	98.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00043	16154	17347	Escherichia_coli_acrA	0/0	100.0	99.2	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	124371	125504	Escherichia_coli_ampC	0/0	100.0	97.7	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00042	27940	29244	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	96.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00007	24730	25887	Escherichia_coli_ampH	0/0	100.0	96.8	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00014	32368	33600	Escherichia_coli_mdfA	0/0	100.0	96.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00012	86957	87571	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00012	87576	91169	evgS	0/0	100.0	96.8	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00028	54226	54954	gadW	0/0	100.0	95.6	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00028	55323	56147	gadX	0/0	100.0	94.3	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00047	28158	28571	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00011	7853	8530	kdpE	0/0	100.0	95.4	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00001	282280	282663	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00025	579	1826	mdtA	0/0	100.0	97.4	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00025	1826	4948	mdtB	0/0	100.0	96.7	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00025	4949	8026	mdtC	0/0	100.0	97.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00028	49568	50725	mdtE	0/0	100.0	98.8	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00028	50750	53863	mdtF	0/0	100.0	98.5	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00016	2669	3895	mdtG	0/0	100.0	98.5	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00023	69659	70867	mdtH	0/0	100.0	97.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00004	57173	58204	mdtN	0/0	100.0	96.4	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00004	55122	57173	mdtO	0/0	100.0	96.3	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00004	53659	55125	mdtP	0/0	100.0	97.5	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00095	69	974	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00008	113378	113852	mphB	0/0	99.6	96.6	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00034	6455	8203	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00005	156039	157007	pmrF	0/0	100.0	98.1	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00072	1652	2491	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00078	704	1519	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00082	1835	2695	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00002	137275	138762	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00005	92900	94543	yojI	0/0	100.0	97.5	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00080	35	895	(AGly)aac3-IId	0/0	100	99.9	EU022314:1-861	(AGly)aac3-IId	NA
contig00072	3038	3826	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00081	1610	2413	(AGly)strA	0/0	100	100.0	AB366441:22458-23261	(AGly)strA	NA
contig00081	774	1610	(AGly)strB	0/0	100	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00042	27940	29244	(Bla)AmpC1_Ecoli	0/0	100	96.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00004	124371	125504	(Bla)AmpC2_Ecoli	0/0	100	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00007	24730	25887	(Bla)ampH_Ecoli	0/0	100	96.8	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00032	28202	29077	(Bla)blaCTX-M-14	0/0	100	100.0	AF252622:1741-2616	(Bla)blaCTX-M-14	NA
contig00082	1835	2695	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00011	50375	52276	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00095	69	974	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00072	1652	2491	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00078	704	1519	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00072	3957	4430	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00080	35	895	aac(3)-IId	0/0	100	100.0	NG_047251.1	aminoglycoside N-acetyltransferase AAC(3)-IId	GENTAMICIN
contig00072	3038	3826	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00081	1610	2437	aph(3’’)-Ib	0/0	100	99.9	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00081	774	1610	aph(6)-Id	0/0	100	99.9	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00032	28202	29077	blaCTX-M-14	0/0	100	100.0	NG_048929.1	class A extended-spectrum beta-lactamase CTX-M-14	CEPHALOSPORIN
contig00004	124371	125504	blaEC-8	0/0	100	98.2	NG_049086.1	cephalosporin-hydrolyzing class C beta-lactamase EC-8	CEPHALOSPORIN
contig00082	1835	2695	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00072	3957	4430	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00095	69	990	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00072	1652	2491	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00078	704	1519	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00080	35	895	AAC3	0/0	100.0	100.0	MEG_64	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00043	16154	17347	ACRA	0/0	100.0	99.2	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00043	12982	16131	ACRB	0/0	100.0	99.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00008	134559	137672	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00017	83805	84962	ACRE	0/0	100.0	98.4	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00017	84974	88078	ACRF	0/0	100.0	97.8	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00017	82744	83406	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00007	24730	25887	AMPH	0/0	100.0	96.8	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00072	3038	3826	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00081	1610	2437	APH3-DPRIME	0/0	100.0	99.9	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00081	774	1610	APH6	0/0	100.0	99.9	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00033	11265	13117	ASMA	0/0	100.0	98.3	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00002	115744	116563	BACA	0/0	99.8	96.7	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00025	10839	11560	BAER	0/0	99.9	98.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00025	9439	10842	BAES	0/0	100.0	96.4	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00005	66439	67629	BCR	0/0	100.0	97.5	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00004	124371	125504	BLAEC	0/0	100.0	98.2	MEG_1278	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00018	22021	22719	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00018	22716	24089	CPXAR	0/0	100.0	98.8	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	15391	16023	CRP	0/0	100.0	99.0	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00032	28196	29099	CTX	0/0	100.0	99.9	MEG_2401	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00072	3957	4430	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00026	16391	17563	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00026	17580	19118	EMRB	0/0	100.0	98.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00015	87427	88617	EMRD	0/0	100.0	97.7	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00012	85378	86541	EMRK	0/0	100.0	98.0	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00026	15734	16264	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00012	83840	85378	EMRY	0/0	100.0	97.5	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00004	80809	82452	EPTA	0/0	100.0	98.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00012	87576	91169	EVGS	0/0	100.0	97.3	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00028	54226	54954	GADW	0/0	100.0	97.8	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00028	55323	56147	GADX	0/0	100.0	94.3	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00047	28158	28571	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00011	7853	8530	KDPE	0/0	100.0	95.4	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00001	282280	282669	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00001	282684	283118	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00014	32368	33600	MDFA	0/0	100.0	98.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00025	579	1826	MDTA	0/0	100.0	97.4	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00025	1826	4948	MDTB	0/0	100.0	96.7	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00025	4949	8026	MDTC	0/0	100.0	97.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00028	49568	50725	MDTE	0/0	100.0	98.8	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00028	50750	53863	MDTF	0/0	100.0	98.5	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00016	2669	3895	MDTG	0/0	100.0	98.7	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00023	69659	70867	MDTH	0/0	100.0	97.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00001	243783	244112	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00001	243431	243796	MDTJ	0/0	100.0	98.1	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00001	172381	173753	MDTK	0/0	99.9	98.2	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00004	57173	58204	MDTN	0/0	100.0	96.4	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00004	55122	57173	MDTO	0/0	100.0	96.3	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00004	53659	55125	MDTP	0/0	100.0	97.5	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00095	69	990	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00008	113378	113852	MPHB	0/0	99.6	96.6	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00034	6455	8203	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00011	50375	52276	PBP2	0/0	100.0	99.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00042	27940	29244	PBP4B	0/0	100.0	96.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00005	156039	157007	PMRF	0/0	100.0	98.1	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00003	232638	233507	ROBA	0/0	100.0	99.5	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00004	31693	32015	SOXS	0/0	99.7	97.5	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00072	1525	2492	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00078	704	1519	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00082	1817	3062	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00005	92900	94543	YOGI	0/0	100.0	97.5	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID045

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00068	391	1266	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00091	91	732	catA2_1	0/0	100.0	96.0	X53796	catA2	Chloramphenicol
contig00066	7607	7993	fosA7_1	0/0	91.5	93.5	LAPJ01000014	fosA7	Fosfomycin
contig00030	29805	31037	mdf(A)_1	0/0	100.0	98.4	Y08743	mdf(A)
contig00072	208	864	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00062	754	2000	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00007	143948	147097	acrB	0/0	100.0	99.2	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	135915	139028	acrD	0/0	100.0	98.6	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00005	203227	204384	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00005	204396	207500	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00005	202166	202828	acrS	0/0	100.0	99.1	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00013	123262	124081	bacA	0/0	99.8	98.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00053	10682	11404	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00053	9282	10685	baeS	0/0	100.0	96.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00091	91	732	catII_from_Escherichia_coli_K-12	0/0	100.0	96.0	X53796.1:186-828	catII is a chloramphenicol acetyltransferase. This particular catII is found in E.coli K-12. Confers resistance to chloramphenicol.	phenicol
contig00020	22613	23986	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00002	267478	268110	CRP	0/0	100.0	99.0	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00068	391	1266	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00051	17471	18643	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00051	18660	20198	emrB	0/0	100.0	99.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00027	9379	10434	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00051	16814	17344	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00027	7841	9379	emrY	0/0	100.0	98.2	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00001	167186	168829	eptA	0/0	100.0	99.3	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00007	147120	148313	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	123829	124962	Escherichia_coli_ampC	0/0	100.0	97.7	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00008	170346	171650	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00007	55729	56886	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00030	29805	31037	Escherichia_coli_mdfA	0/0	100.0	96.8	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00027	10958	11572	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00027	11577	15170	evgS	0/0	100.0	99.1	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00066	7607	7993	FosA7	0/0	91.5	93.5	LAPJ01000014.1:36822-37245	fosA7 is an enzyme that confers resistance to fosfomycin in Escherichia coli by breaking the epoxide ring of the molecule.	fosfomycin
contig00002	97574	98302	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00002	96382	97206	gadX	0/0	100.0	97.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00011	148523	148936	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00015	8002	8674	kdpE	0/0	99.3	97.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00016	97329	97712	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00053	422	1669	mdtA	0/0	100.0	97.6	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00053	1669	4791	mdtB	0/0	100.0	98.3	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00053	4792	7869	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00002	101803	102960	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00002	98665	101778	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00014	125708	126934	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00014	115869	117077	mdtH	0/0	100.0	98.5	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00010	131603	132835	mdtM	0/0	100.0	96.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00001	191492	192523	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00001	192523	194574	mdtO	0/0	100.0	98.8	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00001	194571	196037	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00008	113958	114432	mphB	0/0	99.6	97.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00004	86754	88502	msbA	0/0	100.0	99.3	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00003	124897	125865	pmrF	0/0	100.0	99.5	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00072	208	864	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00089	1043	1405	ramA	0/0	96.8	90.6	JQ727668:0-375	RamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00062	754	2000	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00013	99416	100903	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00003	76214	77857	yojI	0/0	100.0	99.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00008	170346	171650	(Bla)AmpC1_Ecoli	0/0	100.0	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00001	123829	124962	(Bla)AmpC2_Ecoli	0/0	100.0	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00007	55729	56886	(Bla)ampH_Ecoli	0/0	100.0	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00068	391	1266	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00015	60462	62363	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00066	7607	7993	(Fcyn)FosA7	0/0	91.5	93.5	LAPJ01000014:36823-37245	(Fcyn)FosA7	NA
contig00072	208	864	(Flq)qnr-S1	0/0	100.0	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00091	91	732	(Phe)catA2	0/0	100.0	96.0	X53796:187-903	(Phe)catA2	NA
contig00062	754	2028	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00062	73	723	(Tet)tetR	0/0	100.0	100.0	HF545434:53576-54226	(Tet)tetR	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00068	391	1266	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00001	123829	124962	blaEC-18	0/0	100.0	99.2	NG_049083.1	class C extended-spectrum beta-lactamase EC-18	CEPHALOSPORIN
contig00091	91	732	catA2	0/0	100.0	99.8	NG_047596.1	type A-2 chloramphenicol O-acetyltransferase CatII	CHLORAMPHENICOL
contig00066	7607	7993	fosA7.5	0/0	91.5	100.0	NG_067231.1	fosfomycin resistance glutathione transferase FosA7.5	FOSFOMYCIN
contig00072	208	864	qnrS1	0/0	100.0	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00062	829	2028	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00007	147120	148313	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00007	143948	147097	ACRB	0/0	100.0	99.2	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00008	135915	139028	ACRD	0/0	100.0	98.6	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00005	203227	204384	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00005	204396	207500	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00005	202166	202828	ACRS	0/0	100.0	99.1	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00007	55729	56886	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00009	6961	8813	ASMA	0/0	100.0	98.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00013	123262	124081	BACA	0/0	99.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00053	10682	11404	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00053	9282	10685	BAES	0/0	100.0	96.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00003	49755	50945	BCR	0/0	100.0	98.1	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00001	123829	124962	BLAEC	0/0	100.0	99.2	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00091	91	732	CATA	0/0	100.0	99.8	MEG_1568	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00020	21918	22616	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00020	22613	23986	CPXAR	0/0	100.0	99.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00002	267478	268110	CRP	0/0	100.0	99.0	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00051	17471	18643	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00051	18660	20198	EMRB	0/0	100.0	99.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00006	104253	105443	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00027	9379	10542	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00051	16814	17344	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00027	7841	9379	EMRY	0/0	100.0	98.3	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00001	167186	168829	EPTA	0/0	100.0	99.3	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00027	11577	15170	EVGS	0/0	100.0	99.1	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00066	7607	7993	FOSA	0/0	91.5	93.5	MEG_2988	Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA	NA
contig00002	97574	98302	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00002	96382	97206	GADX	0/0	100.0	97.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00011	148523	148936	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00015	8002	8674	KDPE	0/0	99.3	97.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00016	97323	97712	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00016	96875	97309	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00030	29805	31037	MDFA	0/0	100.0	98.5	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00053	422	1669	MDTA	0/0	100.0	97.6	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00053	1669	4791	MDTB	0/0	100.0	98.3	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00053	4792	7869	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00002	101803	102960	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00002	98665	101778	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00014	125708	126934	MDTG	0/0	100.0	99.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00014	115869	117077	MDTH	0/0	100.0	98.5	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00023	32064	32393	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00023	32380	32745	MDTJ	0/0	100.0	99.7	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00037	1343	2716	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00010	131603	132835	MDTM	0/0	100.0	96.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00001	191492	192523	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00001	192523	194574	MDTO	0/0	100.0	98.8	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00001	194571	196037	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00008	113958	114432	MPHB	0/0	99.6	97.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00004	86754	88502	MSBA	0/0	100.0	99.3	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00015	60462	62363	PBP2	0/0	100.0	99.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00008	170346	171650	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00003	124897	125865	PMRF	0/0	100.0	99.5	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00072	208	864	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00089	1043	1405	RAMA	0/0	96.8	90.6	MEG_6044	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:RAMA	NA
contig00010	67934	68803	ROBA	0/0	100.0	99.2	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00001	217653	217976	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00062	754	2028	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00003	76214	77857	YOGI	0/0	100.0	99.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID047

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00111	1696	2556	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00113	1540	2139	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00082	1308	2096	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00088	3970	4773	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00088	3134	3970	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00089	2404	3279	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00113	579	1409	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00082	704	1177	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00015	32470	33702	mdf(A)_1	0/0	100.0	97.9	Y08743	mdf(A)
contig00133	69	990	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00082	2616	3482	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00088	4834	5649	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00088	909	2155	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00111	1696	2556	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00113	1540	2139	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00082	1308	2096	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00025	54140	57289	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	146537	149650	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00005	163425	164582	acrE	0/0	100.0	98.5	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00005	164594	167698	acrF	0/0	100.0	97.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00005	162364	163026	acrS	0/0	100.0	98.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00088	3970	4773	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00088	3134	3970	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00008	114242	115061	bacA	0/0	99.8	98.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00001	99748	100469	baeR	0/0	99.9	98.2	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00001	98348	99751	baeS	0/0	100.0	97.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00020	22913	24286	cpxA	0/0	100.0	98.2	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00018	15385	16017	CRP	0/0	100.0	98.9	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00089	2404	3279	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00082	704	1177	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00009	58704	59876	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00009	59893	61431	emrB	0/0	100.0	98.6	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	414438	415493	emrK	0/0	100.0	98.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00009	58047	58577	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	412900	414438	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00011	100959	102602	eptA	0/0	100.0	97.8	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00025	57312	58505	Escherichia_coli_acrA	0/0	100.0	99.3	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00014	101671	102804	Escherichia_coli_ampC	0/0	100.0	98.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00074	8301	9599	Escherichia_coli_ampC1_beta-lactamase	0/0	99.5	96.1	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00016	14787	15944	Escherichia_coli_ampH	0/0	100.0	98.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00002	20788	21120	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00015	32470	33702	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	416017	416631	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	416636	420229	evgS	0/0	100.0	96.8	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00012	56718	57446	gadW	0/0	100.0	95.5	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00012	55525	56349	gadX	0/0	100.0	94.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00050	21114	21527	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00056	7859	8536	kdpE	0/0	100.0	97.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00017	76818	77201	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00001	89488	90735	mdtA	0/0	100.0	96.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00001	90735	93857	mdtB	0/0	100.0	96.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00001	93858	96935	mdtC	0/0	100.0	97.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00012	60947	62104	mdtE	0/0	100.0	98.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00012	57809	60922	mdtF	0/0	100.0	98.4	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00021	38513	39739	mdtG	0/0	100.0	98.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00021	28674	29882	mdtH	0/0	100.0	98.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00011	77310	78341	mdtN	0/0	100.0	96.4	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00011	75259	77310	mdtO	0/0	100.0	97.4	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00011	73796	75262	mdtP	0/0	100.0	96.7	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00133	69	974	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00004	125356	125830	mphB	0/0	99.6	96.2	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00010	50246	51994	msbA	0/0	100.0	98.7	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00113	579	1409	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00001	299927	300895	pmrF	0/0	100.0	98.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00082	2643	3482	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00088	4834	5649	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00088	909	2155	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00008	90475	91962	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	33341	34507	ugd	0/0	100.0	96.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00001	238174	239817	yojI	0/0	100.0	98.3	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00111	1696	2556	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00082	1308	2096	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00088	3970	4773	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00088	3134	3970	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00074	8301	9599	(Bla)AmpC1_Ecoli	0/0	99.5	96.1	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00014	101671	102804	(Bla)AmpC2_Ecoli	0/0	100.0	98.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00016	14787	15944	(Bla)ampH_Ecoli	0/0	100.0	98.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00089	2404	3279	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00113	579	1409	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00006	28477	30378	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00133	69	974	(MLS)mph(A)	0/0	100.0	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00082	2643	3482	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00088	4834	5649	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00088	881	2155	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00088	2186	2812	(Tet)tetR	1/24	96.3	96.3	HF545434:53576-54226	(Tet)tetR	NA
contig00082	704	1177	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00111	1696	2556	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00113	1540	2094	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00082	1308	2096	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00088	3970	4797	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00088	3134	3970	aph(6)-Id	0/0	100	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00089	2404	3279	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00014	101671	102804	blaEC-8	0/0	100	98.7	NG_049086.1	cephalosporin-hydrolyzing class C beta-lactamase EC-8	CEPHALOSPORIN
contig00113	579	1409	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00082	704	1177	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00133	69	990	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00082	2643	3482	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00088	4834	5649	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00088	881	2080	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00111	1696	2556	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00025	57312	58505	ACRA	0/0	100.0	99.3	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00025	54140	57289	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00004	146537	149650	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00005	163425	164582	ACRE	0/0	100.0	98.5	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00005	164594	167698	ACRF	0/0	100.0	97.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00005	162364	163026	ACRS	0/0	100.0	98.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00016	14787	15944	AMPH	0/0	100.0	98.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00082	1308	2096	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00088	3970	4797	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00088	3134	3970	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00001	74974	76826	ASMA	0/0	100.0	98.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00008	114242	115061	BACA	0/0	99.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00001	99748	100469	BAER	0/0	99.9	98.2	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00001	98348	99751	BAES	0/0	100.0	97.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	211714	212904	BCR	0/0	100.0	96.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00014	101671	102804	BLAEC	0/0	100.0	98.7	MEG_1278	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00020	22218	22916	CPXAR	0/0	100.0	99.3	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00020	22913	24286	CPXAR	0/0	100.0	98.2	MEG_2119	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00018	15385	16017	CRP	0/0	100.0	98.9	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00082	704	1177	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00009	58704	59876	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00009	59893	61431	EMRB	0/0	100.0	98.6	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00013	24887	26077	EMRD	0/0	100.0	97.6	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	414438	415601	EMRK	0/0	100.0	98.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00009	58047	58577	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	412900	414438	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00011	100959	102602	EPTA	0/0	100.0	97.8	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	416636	420229	EVGS	0/0	100.0	97.2	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00012	56718	57446	GADW	0/0	100.0	97.4	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00012	55525	56349	GADX	0/0	100.0	94.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00050	21114	21527	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00056	7859	8536	KDPE	0/0	100.0	97.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00017	76812	77201	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00017	76363	76797	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00015	32470	33702	MDFA	0/0	100.0	98.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00001	89488	90735	MDTA	0/0	100.0	96.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00001	90735	93857	MDTB	0/0	100.0	96.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00001	93858	96935	MDTC	0/0	100.0	97.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00012	60947	62104	MDTE	0/0	100.0	98.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00012	57809	60922	MDTF	0/0	100.0	98.4	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00021	38513	39739	MDTG	0/0	100.0	98.8	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00021	28674	29882	MDTH	0/0	100.0	98.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00027	51282	51611	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00027	50930	51295	MDTJ	0/0	100.0	98.1	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00002	286055	287427	MDTK	0/0	99.9	97.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00011	77310	78341	MDTN	0/0	100.0	96.4	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00011	75259	77310	MDTO	0/0	100.0	97.4	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00011	73796	75262	MDTP	0/0	100.0	96.7	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00133	69	990	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00004	125356	125830	MPHB	0/0	99.6	96.2	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00010	50246	51994	MSBA	0/0	100.0	98.7	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00002	20788	21120	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00113	579	1409	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00006	28477	30378	PBP2	0/0	100.0	99.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00074	8301	9599	PBP4B	0/0	99.5	96.1	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	299927	300895	PMRF	0/0	100.0	98.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00071	5457	6326	ROBA	0/0	100.0	99.3	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00011	51831	52153	SOXS	0/0	99.7	97.8	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00082	2642	3609	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00088	4834	5649	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00088	881	2155	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00001	33341	34507	UGD	0/0	100.0	96.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00001	238174	239817	YOGI	0/0	100.0	98.3	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID050

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	1694	2554	aac(3)-IIa_1	0/0	100	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00096	1539	2138	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00086	1702	2490	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00078	5421	6200	aph(3’’)-Ib_5	0/0	97	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00078	4585	5421	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00085	1224	2099	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00096	578	1408	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00086	2621	3094	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00006	27290	28522	mdf(A)_1	0/0	100	99.9	Y08743	mdf(A)
contig00086	316	1182	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole
contig00078	85	900	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole
contig00080	1998	3203	tet(B)_2	0/0	100	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	1694	2554	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00096	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00086	1702	2490	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00001	40681	43830	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	147293	150406	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00070	5854	8958	acrF	0/0	100.0	100.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00034	600	1262	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00078	5421	6200	APH(3’’)-Ib	0/0	97.0	99.7	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00078	4585	5421	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00002	70353	71172	bacA	0/0	99.8	98.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00052	10967	11689	baeR	0/0	100.0	99.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00052	9567	10970	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00012	61576	62949	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00009	15387	16019	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00085	1224	2099	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00086	2621	3094	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00010	58703	59875	emrA	0/0	100.0	97.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00010	59892	61430	emrB	0/0	100.0	98.6	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00003	178484	179539	emrK	0/0	100.0	98.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00010	58046	58576	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00003	176946	178484	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00007	81590	83233	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00001	39465	40658	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00007	38239	39372	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00005	182292	183596	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	95.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00001	128797	129954	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00006	27290	28522	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00003	180063	180677	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00003	180682	184275	evgS	0/0	100.0	96.8	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00038	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00038	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00033	5297	5710	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00013	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00022	30980	31363	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00052	707	1954	mdtA	0/0	100.0	98.1	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00052	1954	5076	mdtB	0/0	100.0	99.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00052	5077	8154	mdtC	0/0	100.0	97.7	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00038	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00038	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00032	29397	30623	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00032	19561	20769	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00019	70066	71298	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00007	112971	114002	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00007	114002	116053	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00007	116050	117516	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00005	126112	126586	mphB	0/0	99.6	96.2	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00004	86644	88392	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00096	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00003	63971	64939	pmrF	0/0	100.0	98.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00086	316	1155	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00078	85	900	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00080	1998	3203	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00002	46586	48073	tolC	0/0	100.0	99.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00003	2095	3738	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	1694	2554	(AGly)aac3-IIa	0/0	100	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00086	1702	2490	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00078	5421	6200	(AGly)strA	0/0	97	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00078	4585	5421	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00005	182292	183596	(Bla)AmpC1_Ecoli	0/0	100	95.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00007	38239	39372	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00001	128797	129954	(Bla)ampH_Ecoli	0/0	100	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00085	1224	2099	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00096	578	1408	(Bla)blaOXA-1	0/0	100	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00013	60155	62056	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00086	316	1155	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00078	85	900	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00080	1998	3203	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00086	2621	3094	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	1694	2554	aac(3)-IIe	0/0	100.0	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00096	1539	2093	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00086	1702	2490	aadA5	0/0	100.0	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00078	5421	6200	aph(3’’)-Ib	0/0	94.2	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00078	4585	5421	aph(6)-Id	0/0	100.0	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00085	1224	2099	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00007	38239	39372	blaEC-15	0/0	100.0	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00096	578	1408	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00086	2621	3094	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00086	316	1155	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00078	85	900	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00080	1998	3203	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	1694	2554	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00001	39465	40658	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00001	40681	43830	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00005	147293	150406	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00070	5854	8958	ACRF	0/0	100.0	100.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00034	600	1262	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00001	128797	129954	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00086	1702	2490	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00078	5421	6200	APH3-DPRIME	0/0	94.2	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00078	4585	5421	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00041	25297	27149	ASMA	0/0	100.0	97.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00002	70353	71172	BACA	0/0	99.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00052	10967	11689	BAER	0/0	100.0	99.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00052	9567	10970	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00017	67338	68528	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00007	38239	39372	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00012	60881	61579	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00012	61576	62949	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	15387	16019	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00104	62	1004	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00086	2621	3094	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00010	58703	59875	EMRA	0/0	100.0	97.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00010	59892	61430	EMRB	0/0	100.0	98.6	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00036	43241	44431	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00003	178484	179647	EMRK	0/0	100.0	98.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00010	58046	58576	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00003	176946	178484	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00007	81590	83233	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00003	180682	184275	EVGS	0/0	100.0	97.2	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00038	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00038	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00033	5297	5710	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00013	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00022	30974	31363	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00022	30526	30960	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00006	27290	28522	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00052	707	1954	MDTA	0/0	100.0	98.1	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00052	1954	5076	MDTB	0/0	100.0	99.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00052	5077	8154	MDTC	0/0	100.0	97.7	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00038	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00038	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00032	29397	30623	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00032	19561	20769	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00022	63756	64085	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00022	64072	64437	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00021	26477	27850	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00019	70066	71298	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00007	112971	114002	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00007	114002	116053	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00007	116050	117516	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00005	126112	126586	MPHB	0/0	99.6	96.2	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00004	86644	88392	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00096	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00013	60155	62056	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00005	182292	183596	PBP4B	0/0	100.0	95.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00003	63971	64939	PMRF	0/0	100.0	98.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00019	21724	22593	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00007	139132	139455	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00086	189	1156	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00078	85	900	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00080	1998	3203	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00080	3997	4413	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00003	2095	3738	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID051

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00076	6262	7122	aac(3)-IId_1	0/0	100.0	99.9	EU022314	aac(3)-IId	Gentamicin, Tobramycin
contig00003	23454	24329	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00750	109	969	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig03356	161	634	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00666	1490	2063	dfrA7_5	3/4	100.0	98.8	AJ419170	dfrA7	Trimethoprim
contig01612	42	551	dfrA8_1	0/0	100.0	100.0	U10186	dfrA8	Trimethoprim
contig00512	263	1026	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00666	180	1046	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00905	410	1656	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline
contig00794	415	1620	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00076	6262	7122	AAC(3)-IId	0/0	100.0	99.9	EU022314.1:0-861	AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00816	1149	1811	acrS	0/0	100.0	97.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00173	2765	4168	baeS	0/0	100.0	90.1	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig03015	101	719	CRP	0/0	97.8	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00003	23454	24329	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig03356	161	634	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00666	1590	2063	dfrA7	0/0	100.0	100.0	FJ854362:2338-2812	dfrA7 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig01612	42	551	dfrA8	0/0	100.0	100.0	KJ174469:710-1220	dfrA8 is a transposon-encoded dihydrofolate reductase found in Salmonella enterica	diaminopyrimidine
contig01821	312	842	emrR	0/0	100.0	99.2	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00512	289	1034	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00830	225	1418	Escherichia_coli_acrA	0/0	100.0	98.9	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig01727	66	1123	Escherichia_coli_ampC	0/0	93.3	98.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00385	1398	2702	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	95.4	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00665	614	946	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00128	185	3778	evgS	0/0	100.0	96.3	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig01705	608	1021	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00087	5744	6421	kdpE	0/0	100.0	96.6	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00670	39	1271	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00012	4008	4484	mphB	0/0	100.0	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00666	180	1019	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00750	109	969	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00905	410	1656	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00794	415	1620	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00076	6262	7122	(AGly)aac3-IId	0/0	100.0	99.9	EU022314:1-861	(AGly)aac3-IId	NA
contig00385	1398	2702	(Bla)AmpC1_Ecoli	0/0	100.0	95.4	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig01727	66	1123	(Bla)AmpC2_Ecoli	0/0	93.3	98.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00003	23454	24329	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00750	109	969	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00512	289	1026	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00666	180	1019	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00905	410	1684	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00794	415	1620	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig03356	161	634	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA
contig01612	42	551	(Tmt)dfrA8	0/0	100.0	100.0	U10186:711-1220	(Tmt)dfrA8	NA
contig00666	1590	2063	(Tmt)dhfr7	0/0	100.0	100.0	X58425:594-1067	(Tmt)dhfr7	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00076	6262	7122	aac(3)-IId	0/0	100.0	100.0	NG_047251.1	aminoglycoside N-acetyltransferase AAC(3)-IId	GENTAMICIN
contig00003	23454	24329	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig01727	66	1123	blaEC-19	0/0	93.3	99.6	NG_049084.1	class C extended-spectrum beta-lactamase EC-19	CEPHALOSPORIN
contig00750	109	969	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig03356	161	634	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00666	1590	2063	dfrA7	0/0	100.0	100.0	NG_047737.1	trimethoprim-resistant dihydrofolate reductase DfrA7	TRIMETHOPRIM
contig01612	42	551	dfrA8	0/0	100.0	100.0	NG_047741.1	trimethoprim-resistant dihydrofolate reductase DfrA8	TRIMETHOPRIM
contig00512	289	1026	erm(B)	0/0	100.0	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00666	180	1019	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00905	485	1684	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE
contig00794	415	1620	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00076	6262	7122	AAC3	0/0	100.0	100.0	MEG_64	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00830	225	1418	ACRA	0/0	100.0	98.9	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00816	1149	1811	ACRS	0/0	100.0	97.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00173	2765	4168	BAES	0/0	100.0	90.1	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig01259	1	1124	BCR	0/0	94.4	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig01727	66	1123	BLAEC	0/0	93.3	99.6	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig03015	101	719	CRP	0/0	97.8	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00666	1590	2063	DFRA	0/0	100.0	100.0	MEG_2548	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig01612	42	551	DFRA	0/0	100.0	100.0	MEG_2553	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig03356	161	634	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig01821	312	842	EMRR	0/0	100.0	99.2	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00512	263	1026	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00128	185	3778	EVGS	0/0	100.0	97.3	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig01705	608	1021	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00087	5744	6421	KDPE	0/0	100.0	96.6	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00670	39	1271	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00012	4008	4484	MPHB	0/0	100.0	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00665	614	946	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00385	1398	2702	PBP4B	0/0	100.0	95.4	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00666	53	1020	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00750	91	1336	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00905	410	1684	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00794	415	1620	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA

ID052

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00152	71	931	blaSHV-12_1	0/0	100	100.0	KF976405	blaSHV-12	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00027	64704	65564	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00087	1809	2282	dfrA5_1	0/0	100	100.0	X12868	dfrA5	Trimethoprim
contig00127	264	1027	erm(B)_18	2/2	100	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00007	32486	33718	mdf(A)_1	0/0	100	98.0	Y08743	mdf(A)
contig00150	69	999	mph(A)_2	2/10	100	98.6	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00087	445	1311	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00006	166026	169175	acrB	0/0	100.0	99.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00025	11499	14612	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00029	45356	46513	acrE	0/0	100.0	97.5	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00029	46525	49629	acrF	0/0	100.0	97.8	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00029	44295	44957	acrS	0/0	100.0	98.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	140891	141710	bacA	0/0	99.8	97.4	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00004	20578	21300	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00004	19178	20581	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00011	63633	65006	cpxA	0/0	100.0	98.3	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00002	280114	280746	CRP	0/0	100.0	98.9	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00087	1809	2282	dfrA5	0/0	100.0	100.0	DQ278190:0-474	dfrA5 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00050	23051	24223	emrA	0/0	100.0	97.4	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00050	24240	25778	emrB	0/0	100.0	98.2	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00033	19802	20857	emrK	0/0	100.0	98.4	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00050	22394	22924	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00033	18264	19802	emrY	0/0	100.0	97.5	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00010	117851	119494	eptA	0/0	100.0	99.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00127	290	1035	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00006	169198	170391	Escherichia_coli_acrA	0/0	100.0	99.1	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	160219	161352	Escherichia_coli_ampC	0/0	100.0	98.1	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00006	76537	77694	Escherichia_coli_ampH	0/0	100.0	98.6	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00007	32486	33718	Escherichia_coli_mdfA	0/0	100.0	96.5	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00033	21381	21995	evgA	0/0	100.0	99.5	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00033	22000	25593	evgS	0/0	100.0	96.7	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00002	100122	100850	gadW	0/0	100.0	95.5	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00002	98929	99753	gadX	0/0	100.0	94.3	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00054	21273	21686	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00009	7766	8441	kdpE	0/0	99.7	95.7	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00035	42525	42908	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00004	10318	11565	mdtA	0/0	100.0	100.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00004	11565	14687	mdtB	0/0	100.0	99.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00004	14688	17765	mdtC	0/0	100.0	99.8	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00002	104351	105508	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00002	101213	104326	mdtF	0/0	100.0	98.5	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00039	21227	22453	mdtG	0/0	100.0	97.8	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00039	31084	32292	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00066	259	1491	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00010	94231	95262	mdtN	0/0	100.0	96.9	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00010	92180	94231	mdtO	0/0	100.0	96.4	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00010	90717	92183	mdtP	0/0	100.0	97.6	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00150	69	971	mphA	0/0	99.7	99.9	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00023	9166	9640	mphB	0/0	99.6	96.6	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00020	50226	51974	msbA	0/0	100.0	98.7	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00017	5950	6918	pmrF	0/0	100.0	98.7	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00152	71	931	SHV-134	0/0	100.0	99.9	HM559945:0-861	SHV-134 is an extended-spectrum beta-lactamase.	carbapenem, cephalosporin, penam
contig00087	445	1284	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00027	64704	65564	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00001	117379	118866	tolC	0/0	100.0	98.3	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00045	30809	31975	ugd	0/0	100.0	99.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00004	159132	160775	yojI	0/0	100.0	96.6	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00008	160219	161352	(Bla)AmpC2_Ecoli	0/0	100.0	98.1	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00006	76537	77694	(Bla)ampH_Ecoli	0/0	100.0	98.6	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00152	71	931	(Bla)blaSHV-12	0/0	100.0	100.0	FJ685654:24-860	(Bla)blaSHV-12	NA
contig00027	64704	65564	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00009	46838	48739	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00127	290	1027	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00150	69	971	(MLS)mph(A)	0/0	99.7	99.9	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00087	445	1284	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00087	1809	2282	(Tmt)dfrA5	0/0	100.0	100.0	X12868:1306-1779	(Tmt)dfrA5	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00008	160219	161352	blaEC-8	0/0	100	99.8	NG_049086.1	cephalosporin-hydrolyzing class C beta-lactamase EC-8	CEPHALOSPORIN
contig00152	71	931	blaSHV-12	0/0	100	100.0	NG_050590.1	class A extended-spectrum beta-lactamase SHV-12	CEPHALOSPORIN
contig00027	64704	65564	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00087	1809	2282	dfrA5	0/0	100	100.0	NG_051699.1	trimethoprim-resistant dihydrofolate reductase DfrA5	TRIMETHOPRIM
contig00127	290	1027	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00150	69	999	mph(A)	2/10	100	98.6	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00087	445	1284	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00006	169198	170391	ACRA	0/0	100.0	99.1	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00006	166026	169175	ACRB	0/0	100.0	99.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00025	11499	14612	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00029	45356	46513	ACRE	0/0	100.0	97.5	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00029	46525	49629	ACRF	0/0	100.0	97.8	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00029	44295	44957	ACRS	0/0	100.0	98.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00006	76537	77694	AMPH	0/0	100.0	98.6	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00076	10489	12342	ASMA	0/0	100.0	97.7	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00001	140891	141710	BACA	0/0	99.8	97.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00004	20578	21300	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00004	19178	20581	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00004	132672	133862	BCR	0/0	100.0	95.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00008	160219	161352	BLAEC	0/0	100.0	99.8	MEG_1278	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00011	62938	63636	CPXAR	0/0	100.0	99.6	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00011	63633	65006	CPXAR	0/0	100.0	98.5	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00002	280114	280746	CRP	0/0	100.0	98.9	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00087	1809	2282	DFRA	0/0	100.0	100.0	MEG_2546	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00050	23051	24223	EMRA	0/0	100.0	97.4	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00050	24240	25778	EMRB	0/0	100.0	98.2	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00056	1479	2669	EMRD	0/0	100.0	97.2	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00033	19802	20965	EMRK	0/0	100.0	98.5	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00050	22394	22924	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00033	18264	19802	EMRY	0/0	100.0	97.5	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00010	117851	119494	EPTA	0/0	100.0	99.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00127	264	1027	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00033	22000	25593	EVGS	0/0	100.0	97.3	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00002	100122	100850	GADW	0/0	100.0	97.7	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00002	98929	99753	GADX	0/0	100.0	94.3	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00054	21273	21686	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00009	7766	8441	KDPE	0/0	99.7	95.7	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00035	42519	42908	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00035	42070	42504	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00007	32486	33718	MDFA	0/0	100.0	98.1	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00004	10318	11565	MDTA	0/0	100.0	100.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00004	11565	14687	MDTB	0/0	100.0	99.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00004	14688	17765	MDTC	0/0	100.0	99.8	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00002	104351	105508	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00002	101213	104326	MDTF	0/0	100.0	98.5	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00039	21227	22453	MDTG	0/0	100.0	98.2	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00039	31084	32292	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00041	30311	30640	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00041	30627	30992	MDTJ	0/0	100.0	98.6	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00003	194899	196271	MDTK	0/0	99.9	98.4	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00066	259	1491	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00010	94231	95262	MDTN	0/0	100.0	96.9	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00010	92180	94231	MDTO	0/0	100.0	96.4	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00010	90717	92183	MDTP	0/0	100.0	97.6	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00150	69	999	MPHA	2/10	100.0	98.6	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00023	9166	9640	MPHB	0/0	99.6	96.6	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00020	50226	51974	MSBA	0/0	100.0	98.7	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00009	46838	48739	PBP2	0/0	100.0	99.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00017	5950	6918	PMRF	0/0	100.0	98.7	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00005	151816	152685	ROBA	0/0	100.0	97.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00152	25	1028	SHV	0/0	99.7	98.9	MEG_6428	Drugs:betalactams:Class_A_betalactamases:SHV	NA
contig00010	68752	69074	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00087	318	1285	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00027	64337	65582	TEM	0/0	98.3	99.3	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00045	30809	31975	UGD	0/0	100.0	99.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00004	159132	160775	YOGI	0/0	100.0	96.6	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID057

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00031	21738	22613	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00061	1218	2450	mdf(A)_1	0/0	100	99.1	Y08743	mdf(A)
contig00031	27254	27910	qnrS1_1	0/0	100	100.0	AB187515	qnrS1	Ciprofloxacin

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00005	124681	127830	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00035	17245	20358	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00029	8449	9606	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00029	5333	8437	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00029	10005	10667	acrS	0/0	100.0	98.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00067	8182	9001	bacA	0/0	99.8	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00008	11081	11803	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00008	11800	13203	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00036	22414	23787	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00052	15000	15632	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00031	21738	22613	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00063	20022	21194	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00063	21211	22749	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00020	4530	5585	emrK	0/0	100.0	98.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00063	19365	19895	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00020	2992	4530	emrY	0/0	100.0	98.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00048	17465	19108	eptA	0/0	100.0	99.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00005	127853	129046	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00078	8727	9860	Escherichia_coli_ampC	0/0	100.0	97.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00020	63862	65166	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00005	36337	37494	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00046	2507	2839	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00061	1218	2450	Escherichia_coli_mdfA	0/0	100.0	97.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00020	6109	6723	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00020	6728	10321	evgS	0/0	100.0	99.5	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00011	103823	104551	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00011	104919	105743	gadX	0/0	100.0	97.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00009	55089	55502	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00024	8068	8740	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00018	9298	9681	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00008	20816	22063	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00008	17694	20816	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00008	14616	17693	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00011	99165	100322	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00011	100347	103460	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00013	100113	101339	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00013	90274	91482	mdtH	0/0	100.0	98.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00015	4255	5286	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00015	5286	7337	mdtO	0/0	100.0	98.8	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00015	7334	8800	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00037	4214	4690	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00004	51527	53275	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00001	124221	125189	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00031	27254	27910	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00032	36175	37662	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00008	77989	79155	ugd	0/0	100.0	95.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00001	75559	77202	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00020	63862	65166	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00078	8727	9860	(Bla)AmpC2_Ecoli	0/0	100	97.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00005	36337	37494	(Bla)ampH_Ecoli	0/0	100	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00031	21738	22613	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00024	60529	62430	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00031	27254	27910	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00031	21738	22613	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00078	8727	9860	blaEC-13	0/0	100	99.6	NG_049079.1	class C extended-spectrum beta-lactamase EC-13	CEPHALOSPORIN
contig00031	27254	27910	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00005	127853	129046	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00005	124681	127830	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00035	17245	20358	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00029	8449	9606	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00029	5333	8437	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00029	10005	10667	ACRS	0/0	100.0	98.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00005	36337	37494	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00008	33670	35522	ASMA	0/0	100.0	98.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00067	8182	9001	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00008	11081	11803	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00008	11800	13203	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	49097	50287	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00078	8727	9860	BLAEC	0/0	100.0	99.6	MEG_1280	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00036	21719	22417	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00036	22414	23787	CPXAR	0/0	100.0	99.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00052	15000	15632	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00063	20022	21194	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00063	21211	22749	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00007	27098	28288	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00020	4530	5693	EMRK	0/0	100.0	98.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00063	19365	19895	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00020	2992	4530	EMRY	0/0	100.0	98.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00048	17465	19108	EPTA	0/0	100.0	99.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00020	6728	10321	EVGS	0/0	100.0	99.5	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00011	103823	104551	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00011	104919	105743	GADX	0/0	100.0	97.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00009	55089	55502	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00024	8068	8740	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00018	9292	9681	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00018	8844	9278	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00061	1218	2450	MDFA	0/0	100.0	99.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00008	20816	22063	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00008	17694	20816	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00008	14616	17693	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00011	99165	100322	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00011	100347	103460	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00013	100113	101339	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00013	90274	91482	MDTH	0/0	100.0	98.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00018	48327	48656	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00018	48643	49008	MDTJ	0/0	100.0	98.9	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00010	71668	73041	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00015	4255	5286	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00015	5286	7337	MDTO	0/0	100.0	98.8	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00015	7334	8800	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00037	4214	4690	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00004	51527	53275	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00046	2507	2839	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00024	60529	62430	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00020	63862	65166	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	124221	125189	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00031	27254	27910	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00014	11922	12791	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00015	30417	30739	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00008	77989	79155	UGD	0/0	100.0	95.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00001	75559	77202	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID058

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00034	4557	5360	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00034	3721	4557	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00228	3498	4373	blaCTX-M-121_1	0/0	100.0	100.0	JN790862	blaCTX-M-121	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig01175	46	921	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00034	2140	3000	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00821	181	663	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00173	3600	4256	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00034	5421	6236	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00378	1676	2922	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00119	2469	5618	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00168	733	3846	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00034	4557	5360	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00034	3721	4557	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00439	922	1743	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00595	1173	1895	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00555	429	1802	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00228	3498	4373	CTX-M-121	0/0	100.0	100.0	JN790862:244-1120	CTX-M-121 is a beta-lactamase found in Escherichia coli	cephalosporin
contig01175	46	921	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00821	181	663	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00658	1051	2150	emrA	0/0	93.8	99.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00327	2290	3345	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00658	394	924	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00327	752	2290	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00119	1253	2446	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00347	1062	2219	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00117	3826	4158	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig01773	225	839	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00500	1981	2691	gadW	0/0	97.5	94.5	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00500	789	1613	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig01162	154	567	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00312	1550	2707	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00015	3182	4408	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00056	6447	7478	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00056	4396	6447	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00056	2933	4399	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00576	1090	1564	mphB	0/0	99.6	97.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig01927	170	646	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00022	7330	9078	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00193	2029	2997	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00173	3600	4256	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00034	5421	6236	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00034	2140	3000	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00378	1676	2922	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00003	8582	9748	ugd	0/0	100.0	95.6	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00007	4872	6038	ugd	0/0	100.0	96.1	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00034	4557	5360	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00034	3721	4557	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00347	1062	2219	(Bla)ampH_Ecoli	0/0	100	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00228	3498	4373	(Bla)blaCTX-M-121	0/0	100	100.0	JN790862:245-1120	(Bla)blaCTX-M-121	NA
contig01175	46	921	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00034	2140	3000	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00173	3600	4256	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00034	5421	6236	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00378	1648	2922	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00821	181	654	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00034	4557	5384	aph(3’’)-Ib	0/0	100	100	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00034	3721	4557	aph(6)-Id	0/0	100	100	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00228	3498	4373	blaCTX-M-121	0/0	100	100	NG_048914.1	class A extended-spectrum beta-lactamase CTX-M-121	CEPHALOSPORIN
contig01175	46	921	blaCTX-M-15	0/0	100	100	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00034	2140	3000	blaTEM-1	0/0	100	100	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00821	181	654	dfrA14	0/0	100	100	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00173	3600	4256	qnrS1	0/0	100	100	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00034	5421	6236	sul2	0/0	100	100	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00378	1648	2847	tet(A)	0/0	100	100	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00119	1253	2446	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00119	2469	5618	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00168	733	3846	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00347	1062	2219	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00034	4557	5384	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00034	3721	4557	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00439	922	1743	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00595	1173	1895	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00174	1152	2342	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00555	429	1802	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00228	2521	3463	CTX	0/0	100.0	98.9	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00228	3492	4395	CTX	0/0	100.0	99.7	MEG_2401	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00821	181	654	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00658	1051	2150	EMRA	0/0	93.8	99.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00327	2290	3453	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00658	394	924	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00327	752	2290	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00500	1981	2691	GADW	0/0	97.5	99.9	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00500	789	1613	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig01162	154	567	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig01127	916	1350	MARR	0/0	100.0	98.4	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig02203	193	627	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00312	1550	2707	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00015	3182	4408	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00390	1297	1626	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00390	945	1310	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00056	6447	7478	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00056	4396	6447	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00056	2933	4399	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00576	1090	1564	MPHB	0/0	99.6	97.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig01927	170	646	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00022	7330	9078	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00117	3826	4158	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00193	2029	2997	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00173	3600	4256	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00604	1660	1982	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00034	5421	6236	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00034	1773	3018	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00378	1648	2922	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00003	8582	9748	UGD	0/0	100.0	95.6	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00007	4872	6038	UGD	0/0	100.0	96.1	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA

ID066

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00064	2526	3327	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00066	919	1722	aph(3’’)-Ib_5	0/0	100.0	99.9	AF321551	aph(3’’)-Ib	Streptomycin
contig00066	83	919	aph(6)-Id_1	0/0	100.0	99.8	M28829	aph(6)-Id	Streptomycin
contig00061	427	1302	blaCTX-M-27_1	0/0	100.0	100.0	AY156923	blaCTX-M-27	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00086	109	969	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00056	1	660	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig00064	3725	4222	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00107	4	486	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00070	266	1029	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00010	78274	79506	mdf(A)_1	0/0	100.0	98.5	Y08743	mdf(A)
contig00059	4118	5048	mph(A)_2	2/10	100.0	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00064	1182	2048	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00066	1783	2598	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00071	1097	2301	tet(B)_2	0/0	99.9	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00064	2526	3305	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00011	73090	76239	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	135661	138774	acrD	0/0	100.0	99.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00014	114452	115609	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00014	115621	118725	acrF	0/0	100.0	98.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00014	113391	114053	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00066	919	1722	APH(3’’)-Ib	0/0	100.0	99.6	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00066	83	919	APH(6)-Id	0/0	100.0	99.6	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00002	77356	78175	bacA	0/0	99.8	98.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00022	48811	49533	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00022	47411	48814	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00056	1	660	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00023	67580	68953	cpxA	0/0	100.0	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00004	15000	15632	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00061	427	1302	CTX-M-27	0/0	100.0	100.0	AY156923:0-876	CTX-M-27 is a beta-lactamase found in Escherichia coli	cephalosporin
contig00064	3725	4222	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00107	4	486	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00025	59204	60376	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00025	60393	61931	emrB	0/0	100.0	99.2	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00003	208568	209623	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00025	58547	59077	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00003	207030	208568	emrY	0/0	100.0	98.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00009	136387	138030	eptA	0/0	100.0	99.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00070	292	1037	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00011	71874	73067	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00009	180237	181370	Escherichia_coli_ampC	0/0	100.0	97.5	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00008	169892	171196	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00011	161111	162268	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00010	78274	79506	Escherichia_coli_mdfA	0/0	100.0	96.9	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00003	210147	210761	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00003	210766	214359	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00004	181934	182662	gadW	0/0	100.0	94.8	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00004	183030	183854	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00007	204568	204981	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00013	8162	8834	kdpE	0/0	99.3	97.3	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00016	52571	52954	marA	0/0	100.0	99.2	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00022	38551	39798	mdtA	0/0	100.0	98.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00022	39798	42920	mdtB	0/0	100.0	98.7	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00022	42921	45998	mdtC	0/0	100.0	98.2	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00004	177276	178433	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00004	178458	181571	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00005	176904	178130	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00005	167065	168273	mdtH	0/0	100.0	98.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00012	117206	118438	mdtM	0/0	100.0	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00009	112702	113733	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00009	110651	112702	mdtO	0/0	100.0	98.7	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00009	109188	110654	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00059	4146	5048	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00008	113908	114382	mphB	0/0	99.6	97.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00018	24523	26271	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00003	57890	58858	pmrF	0/0	100.0	99.7	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00064	1182	2021	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00066	1783	2598	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00086	109	969	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00071	1097	2301	tet(B)	0/0	99.9	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00002	100534	102021	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00003	2012	3655	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00064	2526	3305	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00066	919	1722	(AGly)strA	0/0	100.0	99.8	AB366441:22458-23261	(AGly)strA	NA
contig00066	83	919	(AGly)strB	0/0	100.0	99.8	FJ474091:264-1100	(AGly)strB	NA
contig00008	169892	171196	(Bla)AmpC1_Ecoli	0/0	100.0	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00009	180237	181370	(Bla)AmpC2_Ecoli	0/0	100.0	97.5	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00011	161111	162268	(Bla)ampH_Ecoli	0/0	100.0	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00061	427	1302	(Bla)blaCTX-M-27	0/0	100.0	100.0	AY156923:1-876	(Bla)blaCTX-M-27	NA
contig00086	109	969	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00013	60623	62524	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00070	292	1029	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00059	4146	5048	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00056	1	660	(Phe)catA1	0/0	100.0	99.8	V00622:244-903	(Phe)catA1	NA
contig00064	1182	2021	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00066	1783	2598	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00071	1097	2301	(Tet)tetB	0/0	99.9	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00064	3725	4222	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA
contig00107	4	477	(Tmt)dfrA14	0/0	100.0	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00064	2526	3317	aadA2	0/0	100.0	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00066	919	1746	aph(3’’)-Ib	0/0	100.0	99.9	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00066	83	919	aph(6)-Id	0/0	100.0	99.9	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00061	427	1302	blaCTX-M-27	0/0	100.0	100.0	NG_048976.1	class A extended-spectrum beta-lactamase CTX-M-27	CEPHALOSPORIN
contig00009	180237	181370	blaEC-18	0/0	100.0	99.2	NG_049083.1	class C extended-spectrum beta-lactamase EC-18	CEPHALOSPORIN
contig00086	109	969	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00056	1	660	catA1	0/0	100.0	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00064	3725	4222	dfrA12	0/0	100.0	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00107	4	477	dfrA14	0/0	100.0	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00070	292	1029	erm(B)	0/0	100.0	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00059	4118	5048	mph(A)	2/10	100.0	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00064	1182	2021	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00066	1783	2598	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00071	1097	2301	tet(B)	0/0	99.9	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00011	71874	73067	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00011	73090	76239	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00008	135661	138774	ACRD	0/0	100.0	99.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00014	114452	115609	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00014	115621	118725	ACRF	0/0	100.0	98.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00014	113391	114053	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00011	161111	162268	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00064	2526	3327	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00066	919	1746	APH3-DPRIME	0/0	100.0	99.9	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00066	83	919	APH6	0/0	100.0	99.9	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00022	24763	26616	ASMA	0/0	100.0	96.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00002	77356	78175	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00022	48811	49533	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00022	47411	48814	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00017	85269	86459	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00009	180237	181370	BLAEC	0/0	100.0	99.2	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00056	1	660	CATA	0/0	100.0	100.0	MEG_1584	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00023	66885	67583	CPXAR	0/0	100.0	99.7	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00023	67580	68953	CPXAR	0/0	100.0	99.4	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00004	15000	15632	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00061	405	1308	CTX	0/0	100.0	99.8	MEG_2401	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00061	1337	2279	CTX	0/0	100.0	100.0	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00064	3725	4222	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00107	4	477	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00025	59204	60376	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00025	60393	61931	EMRB	0/0	100.0	99.2	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00006	131531	132721	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00003	208568	209731	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00025	58547	59077	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00003	207030	208568	EMRY	0/0	100.0	98.8	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00009	136387	138030	EPTA	0/0	100.0	99.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00070	266	1029	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00003	210766	214359	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00004	181934	182662	GADW	0/0	100.0	99.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00004	183030	183854	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00007	204568	204981	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00013	8162	8834	KDPE	0/0	99.3	97.3	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00016	52565	52954	MARA	0/0	100.0	99.2	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00016	52117	52551	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00010	78274	79506	MDFA	0/0	100.0	98.5	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00022	38551	39798	MDTA	0/0	100.0	98.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00022	39798	42920	MDTB	0/0	100.0	98.7	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00022	42921	45998	MDTC	0/0	100.0	98.2	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00004	177276	178433	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00004	178458	181571	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00005	176904	178130	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00005	167065	168273	MDTH	0/0	100.0	98.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00016	91600	91929	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00016	91916	92281	MDTJ	0/0	100.0	98.1	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00001	335484	336857	MDTK	0/0	100.0	99.1	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00012	117206	118438	MDTM	0/0	100.0	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00009	112702	113733	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00009	110651	112702	MDTO	0/0	100.0	98.7	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00009	109188	110654	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00059	4118	5048	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00008	113908	114382	MPHB	0/0	99.6	97.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00018	24523	26271	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00013	60623	62524	PBP2	0/0	100.0	99.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00008	169892	171196	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00003	57890	58858	PMRF	0/0	100.0	99.7	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00012	47447	48316	ROBA	0/0	100.0	99.4	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00009	87250	87572	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00064	1055	2022	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00066	1783	2598	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00071	1097	2301	TETB	0/0	99.9	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00003	2012	3655	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID070

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00118	1695	2555	aac(3)-IIa_1	0/0	100	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00122	1539	2138	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00107	1702	2490	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00110	221	1096	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00122	578	1408	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00107	2621	3094	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00029	30138	31370	mdf(A)_1	0/0	100	99.9	Y08743	mdf(A)
contig00111	2639	3560	mph(A)_2	1/1	100	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00107	316	1182	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole
contig00104	1718	2923	tet(B)_2	0/0	100	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00118	1695	2555	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00122	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00107	1702	2490	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00008	39134	42283	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	375904	379017	acrD	0/0	100.0	98.9	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00007	121749	122906	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00007	122918	126022	acrF	0/0	100.0	100.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00007	120688	121350	acrS	0/0	100.0	99.4	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00010	52778	53597	bacA	0/0	99.8	98.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00035	29069	29791	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00035	27669	29072	baeS	0/0	100.0	99.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00046	23043	24416	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00018	15081	15713	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00110	221	1096	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00107	2621	3094	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00050	5195	6367	emrA	0/0	100.0	98.3	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00050	3640	5178	emrB	0/0	100.0	99.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	284150	285205	emrK	0/0	100.0	99.2	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00050	6494	7024	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	282612	284150	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00003	120144	121787	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00008	37918	39111	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	164009	165142	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	343482	344786	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00008	127250	128407	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00034	46369	46701	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00029	30138	31370	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	285729	286343	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	286348	289941	evgS	0/0	100.0	99.6	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00036	41068	41796	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00036	42164	42988	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00048	25271	25684	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00057	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00023	40695	41078	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00035	18809	20056	mdtA	0/0	100.0	97.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00035	20056	23178	mdtB	0/0	100.0	99.7	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00035	23179	26256	mdtC	0/0	100.0	99.8	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00036	36410	37567	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00036	37592	40705	mdtF	0/0	100.0	98.5	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00056	16616	17842	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00005	2605	3813	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00053	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00003	89475	90506	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00003	87424	89475	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00003	85961	87427	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00111	2655	3560	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00001	400293	400767	mphB	0/0	99.6	97.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00004	23577	25325	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00122	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00001	169035	170003	pmrF	0/0	100.0	99.5	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00107	316	1155	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00104	1718	2923	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00010	28929	30416	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	120452	122095	yojI	0/0	100.0	98.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00118	1695	2555	(AGly)aac3-IIa	0/0	100	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00107	1702	2490	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00001	343482	344786	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00003	164009	165142	(Bla)AmpC2_Ecoli	0/0	100	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00008	127250	128407	(Bla)ampH_Ecoli	0/0	100	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00110	221	1096	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00122	578	1408	(Bla)blaOXA-1	0/0	100	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00015	30073	31974	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00111	2655	3560	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00107	316	1155	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00104	1718	2923	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00107	2621	3094	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00118	1695	2555	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00122	1539	2093	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00107	1702	2490	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00110	221	1096	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00003	164009	165142	blaEC	0/0	100	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00122	578	1408	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00107	2621	3094	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00111	2639	3560	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00107	316	1155	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00104	1718	2923	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00118	1695	2555	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00008	37918	39111	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00008	39134	42283	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00001	375904	379017	ACRD	0/0	100.0	98.9	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00007	121749	122906	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00007	122918	126022	ACRF	0/0	100.0	100.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00007	120688	121350	ACRS	0/0	100.0	99.4	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00003	164009	165142	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00008	127250	128407	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00107	1702	2490	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00035	5018	6870	ASMA	0/0	100.0	97.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00010	52778	53597	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00035	29069	29791	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00035	27669	29072	BAES	0/0	100.0	99.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	93990	95180	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00046	22348	23046	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00046	23043	24416	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00018	15081	15713	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00139	61	987	CTX	0/0	98.3	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00107	2621	3094	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00050	5195	6367	EMRA	0/0	100.0	98.3	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00050	3640	5178	EMRB	0/0	100.0	99.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00024	16466	17656	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	284150	285313	EMRK	0/0	100.0	99.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00050	6494	7024	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	282612	284150	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00003	120144	121787	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	286348	289941	EVGS	0/0	100.0	99.6	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00036	41068	41796	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00036	42164	42988	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00048	25271	25684	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00057	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00023	40689	41078	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00023	40241	40675	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00029	30138	31370	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00035	18809	20056	MDTA	0/0	100.0	97.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00035	20056	23178	MDTB	0/0	100.0	99.7	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00035	23179	26256	MDTC	0/0	100.0	99.8	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00036	36410	37567	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00036	37592	40705	MDTF	0/0	100.0	98.5	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00056	16616	17842	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00005	2605	3813	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00028	21818	22147	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00028	22134	22499	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00002	264518	265891	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00053	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00003	89475	90506	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00003	87424	89475	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00003	85961	87427	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00111	2639	3560	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00001	400293	400767	MPHB	0/0	99.6	97.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00004	23577	25325	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00034	46369	46701	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00122	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00015	30073	31974	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	343482	344786	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	169035	170003	PMRF	0/0	100.0	99.5	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00037	19925	20794	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00003	64021	64344	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00107	189	1156	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00104	1718	2923	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00104	3717	4133	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00001	120452	122095	YOGI	0/0	100.0	98.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID073

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00185	71	931	blaSHV-12_1	0/0	100	100.0	KF976405	blaSHV-12	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00165	395	1255	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00157	264	1027	erm(B)_18	2/2	100	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00029	16291	17523	mdf(A)_1	0/0	100	98.6	Y08743	mdf(A)

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	80246	83395	acrB	0/0	100.0	99.3	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00030	37677	40790	acrD	0/0	100.0	99.3	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00013	79239	80396	acrE	0/0	100.0	99.1	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00013	80408	83512	acrF	0/0	100.0	98.5	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00013	78178	78840	acrS	0/0	100.0	99.1	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00009	69268	70089	bacA	0/0	100.0	98.4	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00011	80989	81711	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00011	79589	80992	baeS	0/0	100.0	93.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00008	8959	10332	cpxA	0/0	100.0	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00002	42025	42657	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00063	14748	15920	emrA	0/0	100.0	98.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00063	15937	17475	emrB	0/0	100.0	98.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00056	7518	8573	emrK	0/0	100.0	98.4	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00063	14091	14621	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00056	5980	7518	emrY	0/0	100.0	98.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00007	53018	54661	eptA	0/0	100.0	98.8	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00157	290	1035	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00003	83418	84611	Escherichia_coli_acrA	0/0	100.0	99.9	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00007	96718	97851	Escherichia_coli_ampC	0/0	100.0	98.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00023	44869	46173	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	96.3	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00027	12330	13487	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00029	16291	17523	Escherichia_coli_mdfA	0/0	100.0	97.1	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00056	9096	9710	evgA	0/0	100.0	99.7	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00056	9715	13308	evgS	0/0	100.0	97.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00028	35258	35986	gadW	0/0	100.0	94.9	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00028	34066	34890	gadX	0/0	100.0	98.1	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00024	24031	24444	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00021	11168	11845	kdpE	0/0	100.0	96.6	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00033	31485	31868	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00011	71976	75098	mdtB	0/0	100.0	98.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00011	75099	78176	mdtC	0/0	100.0	98.9	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00028	39487	40644	mdtE	0/0	100.0	99.3	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00028	36349	39462	mdtF	0/0	100.0	99.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00004	132356	133582	mdtG	0/0	100.0	98.5	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00004	122517	123725	mdtH	0/0	100.0	99.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00034	35718	36950	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00007	19557	20588	mdtN	0/0	100.0	98.6	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00007	17506	19557	mdtO	0/0	100.0	97.5	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00007	16046	17509	mdtP	1/3	99.8	98.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00030	16486	16960	mphB	0/0	99.6	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00014	49560	51308	msbA	0/0	100.0	98.9	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00006	124902	125870	pmrF	0/0	100.0	98.7	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00185	71	931	SHV-134	0/0	100.0	99.9	HM559945:0-861	SHV-134 is an extended-spectrum beta-lactamase.	carbapenem, cephalosporin, penam
contig00165	395	1255	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00009	50633	52120	tolC	0/0	100.0	98.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00006	74481	76124	yojI	0/0	100.0	99.5	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00023	44869	46173	(Bla)AmpC1_Ecoli	0/0	100	96.3	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00007	96718	97851	(Bla)AmpC2_Ecoli	0/0	100	98.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00027	12330	13487	(Bla)ampH_Ecoli	0/0	100	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00185	71	931	(Bla)blaSHV-12	0/0	100	100.0	FJ685654:24-860	(Bla)blaSHV-12	NA
contig00165	395	1255	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00021	61939	63840	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.8	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00157	290	1027	(MLS)erm(B)	0/0	100	99.6	M11180:714-1451	(MLS)erm(B)	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00007	96718	97851	blaEC	0/0	100	99.1	NG_047496.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00185	71	931	blaSHV-12	0/0	100	100.0	NG_050590.1	class A extended-spectrum beta-lactamase SHV-12	CEPHALOSPORIN
contig00165	395	1255	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00157	290	1027	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	83418	84611	ACRA	0/0	100.0	99.9	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00003	80246	83395	ACRB	0/0	100.0	99.3	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00030	37677	40790	ACRD	0/0	100.0	99.3	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00013	79239	80396	ACRE	0/0	100.0	99.1	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00013	80408	83512	ACRF	0/0	100.0	98.5	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00013	78178	78840	ACRS	0/0	100.0	99.1	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00027	12330	13487	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00009	69268	70089	BACA	0/0	100.0	98.7	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00011	80989	81711	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00011	79589	80992	BAES	0/0	100.0	93.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00006	47795	48985	BCR	0/0	100.0	97.1	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00007	96718	97851	BLAEC	0/0	100.0	99.1	MEG_1276	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00008	8959	10332	CPXAR	0/0	100.0	98.9	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00008	10329	11027	CPXAR	0/0	100.0	99.7	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00002	42025	42657	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00063	14748	15920	EMRA	0/0	100.0	98.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00063	15937	17475	EMRB	0/0	100.0	98.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00037	29091	30281	EMRD	0/0	100.0	98.3	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00056	7518	8681	EMRK	0/0	100.0	98.5	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00063	14091	14621	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00056	5980	7518	EMRY	0/0	100.0	98.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00007	53018	54661	EPTA	0/0	100.0	98.8	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00157	264	1027	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00056	9715	13308	EVGS	0/0	100.0	98.8	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00028	35258	35986	GADW	0/0	100.0	99.2	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00028	34066	34890	GADX	0/0	100.0	98.1	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00024	24031	24444	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00021	11168	11845	KDPE	0/0	100.0	96.6	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00033	31479	31868	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00033	31030	31464	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00029	16291	17523	MDFA	0/0	100.0	98.7	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00011	71976	75098	MDTB	0/0	100.0	98.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00011	75099	78176	MDTC	0/0	100.0	98.9	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00028	39487	40644	MDTE	0/0	100.0	99.3	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00028	36349	39462	MDTF	0/0	100.0	99.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00004	132356	133582	MDTG	0/0	100.0	98.8	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00004	122517	123725	MDTH	0/0	100.0	99.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00068	1754	2083	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00068	2070	2434	MDTJ	0/0	99.7	99.2	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00020	33769	35142	MDTK	0/0	100.0	99.4	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00034	35718	36950	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00007	19557	20588	MDTN	0/0	100.0	98.6	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00007	17506	19557	MDTO	0/0	100.0	97.5	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00007	16046	17509	MDTP	1/3	99.8	98.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00030	16486	16960	MPHB	0/0	99.6	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00014	49560	51308	MSBA	0/0	100.0	98.9	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00021	61939	63840	PBP2	0/0	100.0	98.8	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00023	44869	46173	PBP4B	0/0	100.0	96.3	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00006	124902	125870	PMRF	0/0	100.0	98.7	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00040	29575	30444	ROBA	0/0	100.0	98.8	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00185	25	1028	SHV	0/0	99.7	98.9	MEG_6428	Drugs:betalactams:Class_A_betalactamases:SHV	NA
contig00054	4339	4661	SOXS	0/0	99.7	98.8	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00006	74481	76124	YOGI	0/0	100.0	99.5	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID081

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00112	1539	2138	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00096	1702	2490	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00084	5421	6200	aph(3’’)-Ib_5	0/0	97	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00084	4585	5421	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00095	1222	2097	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00112	578	1408	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00096	2621	3094	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00005	64055	65287	mdf(A)_1	0/0	100	99.9	Y08743	mdf(A)
contig00122	68	989	mph(A)_2	1/1	100	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00096	316	1182	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole
contig00084	85	900	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole
contig00087	1998	3203	tet(B)_2	0/0	100	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00112	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00096	1702	2490	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00027	39300	42449	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	148083	151196	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00077	5525	8629	acrF	0/0	100.0	100.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00063	20452	21114	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00084	5421	6200	APH(3’’)-Ib	0/0	97.0	99.7	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00084	4585	5421	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00010	70354	71173	bacA	0/0	99.8	98.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00026	57251	57973	baeR	0/0	100.0	99.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00026	55851	57254	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00051	23029	24402	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00009	15387	16019	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00095	1222	2097	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00096	2621	3094	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00007	58703	59875	emrA	0/0	100.0	97.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00007	59892	61430	emrB	0/0	100.0	98.6	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	270703	271758	emrK	0/0	100.0	98.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00007	58046	58576	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	269165	270703	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00060	7687	9330	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00027	38084	39277	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00038	29763	30896	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00059	25513	26811	Escherichia_coli_ampC1_beta-lactamase	0/0	99.5	96.1	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00018	65498	66655	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00005	64055	65287	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	272282	272896	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	272901	276494	evgS	0/0	100.0	96.8	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00043	2243	2971	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00043	1051	1875	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00039	5312	5725	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00064	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00023	30981	31364	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00026	46991	48238	mdtA	0/0	100.0	98.1	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00026	48238	51360	mdtB	0/0	100.0	99.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00026	51361	54438	mdtC	0/0	100.0	97.7	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00043	6472	7629	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00043	3334	6447	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00035	29397	30623	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00035	19561	20769	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00036	28265	29497	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00019	60675	61706	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00019	58624	60675	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00019	57161	58627	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00122	68	973	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00003	126902	127376	mphB	0/0	99.6	96.2	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00004	51374	53122	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00112	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00001	156190	157158	pmrF	0/0	100.0	98.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00096	316	1155	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00084	85	900	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00087	1998	3203	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00010	46587	48074	tolC	0/0	100.0	99.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	94315	95958	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00096	1702	2490	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00084	5421	6200	(AGly)strA	0/0	97.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00084	4585	5421	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00059	25513	26811	(Bla)AmpC1_Ecoli	0/0	99.5	96.1	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00038	29763	30896	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00018	65498	66655	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00095	1222	2097	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00112	578	1408	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00012	38461	40362	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00122	68	973	(MLS)mph(A)	0/0	100.0	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00096	316	1155	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00084	85	900	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00087	1998	3203	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00096	2621	3094	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00112	1539	2093	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00096	1702	2490	aadA5	0/0	100.0	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00084	5421	6200	aph(3’’)-Ib	0/0	94.2	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00084	4585	5421	aph(6)-Id	0/0	100.0	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00095	1222	2097	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00038	29763	30896	blaEC-15	0/0	100.0	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00112	578	1408	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00096	2621	3094	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00122	68	989	mph(A)	1/1	100.0	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00096	316	1155	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00084	85	900	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00087	1998	3203	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00027	38084	39277	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00027	39300	42449	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00003	148083	151196	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00077	5525	8629	ACRF	0/0	100.0	100.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00063	20452	21114	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00018	65498	66655	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00096	1702	2490	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00084	5421	6200	APH3-DPRIME	0/0	94.2	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00084	4585	5421	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00026	32873	34725	ASMA	0/0	100.0	97.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00010	70354	71173	BACA	0/0	99.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00026	57251	57973	BAER	0/0	100.0	99.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00026	55851	57254	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	67338	68528	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00038	29763	30896	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00051	22334	23032	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00051	23029	24402	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	15387	16019	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00125	62	1004	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00096	2621	3094	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00007	58703	59875	EMRA	0/0	100.0	97.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00007	59892	61430	EMRB	0/0	100.0	98.6	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00040	43174	44364	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	270703	271866	EMRK	0/0	100.0	98.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00007	58046	58576	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	269165	270703	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00060	7687	9330	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	272901	276494	EVGS	0/0	100.0	97.2	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00043	2243	2971	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00043	1051	1875	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00039	5312	5725	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00064	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00023	30975	31364	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00023	30527	30961	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00005	64055	65287	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00026	46991	48238	MDTA	0/0	100.0	98.1	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00026	48238	51360	MDTB	0/0	100.0	99.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00026	51361	54438	MDTC	0/0	100.0	97.7	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00043	6472	7629	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00043	3334	6447	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00035	29397	30623	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00035	19561	20769	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00023	63757	64086	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00023	64073	64438	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00014	26477	27850	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00036	28265	29497	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00019	60675	61706	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00019	58624	60675	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00019	57161	58627	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00122	68	989	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00003	126902	127376	MPHB	0/0	99.6	96.2	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00004	51374	53122	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00112	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00012	38461	40362	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00059	25513	26811	PBP4B	0/0	99.5	96.1	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	156190	157158	PMRF	0/0	100.0	98.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00045	21724	22593	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00019	35222	35545	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00096	189	1156	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00084	85	900	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00087	1998	3203	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00087	3997	4413	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00001	94315	95958	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID096I

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00122	5182	6042	aac(3)-IIa_1	0/0	100.0	100.0	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00122	9866	10741	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00137	9040	9906	blaSHV-187_1	0/0	100.0	99.5	LN515533	blaSHV-187
contig00122	6184	7044	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00233	425	1084	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig00202	4742	5315	dfrA7_5	3/4	100.0	98.8	AJ419170	dfrA7	Trimethoprim
contig00075	12852	13271	fosA_3	0/0	100.0	99.8	ACWO01000079	fosA	Fosfomycin
contig00017	10037	11212	oqxA_1	0/0	100.0	99.4	EU370913	oqxA	Nalidixic_acid, Ciprofloxacin
contig00017	6861	10013	oqxB_1	0/0	100.0	99.2	EU370913	oqxB	Nalidixic_acid, Ciprofloxacin
contig00202	3432	4298	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00257	860	2106	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00122	5182	6042	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00233	425	1084	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00122	9866	10741	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00202	4842	5315	dfrA7	0/0	100.0	100.0	FJ854362:2338-2812	dfrA7 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00075	12852	13271	FosA6	0/0	100.0	99.5	KU254579.1:59421-59841	fosA6 is a plasmid-encoded enzyme that confers resistance to fosfomycin in Escherichia coli by breaking the epoxide ring of the molecule.	fosfomycin
contig00010	8294	9487	Klebsiella_pneumoniae_acrA	2/3	99.8	97.7	AJ318073.1:793-1990	AcrA is a subunit of the AcrAB multidrug efflux system that in K. pneumoniae which is encoded by the acrRAB operon.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00063	3564	3926	Klebsiella_pneumoniae_KpnE	0/0	100.0	99.2	AP006725.1:2483889-2484252	KpnE subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan	aminoglycoside, cephalosporin, macrolide, peptide, rifamycin, tetracycline
contig00063	3913	4242	Klebsiella_pneumoniae_KpnF	0/0	100.0	100.0	AP006725.1:2484238-2484568	KpnF subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan.	aminoglycoside, cephalosporin, macrolide, peptide, rifamycin, tetracycline
contig00113	10340	11512	Klebsiella_pneumoniae_KpnG	0/0	100.0	99.3	ACWO01000051.1:22092-23265	KpnG consists of ~390 residues and resembles EmrA of E. coli. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin ceftazidime ciprofloxacin ertapenem erythromycin gentamicin imipenem ticarcillin norfloxacin polymyxin-B piperacillin spectinomycin tobramycin and streptomycin	aminoglycoside, carbapenem, cephalosporin, fluoroquinolone, macrolide, penam, penem, peptide
contig00059	13299	14453	Klebsiella_pneumoniae_OmpK37	7/32	99.9	95.2	AJ011502.1:300-1425	Klebsiella pneumoniae outer membrane porin protein. Is preferentially detected in porin-deficient strains. Functional characterization of this new porin revealed a narrower pore than those of porins OmpK35 and OmpK36 which did not allow penetration by certain beta-lactams. Also when a resistant strain expresses porin OmpK37 is less susceptible to cefotaxime and cefoxitin than when it is expressing either OmpK36 or OmpK35.	carbapenem, cephalosporin, cephamycin, monobactam, penam, penem
contig00017	10037	11212	oqxA	0/0	100.0	99.4	EU370913.1:46651-47827	RND efflux pump conferring resistance to fluoroquinolone	diaminopyrimidine, fluoroquinolone, glycylcycline, nitrofuran, tetracycline
contig00017	6861	10013	oqxB	0/0	100.0	99.2	EU370913.1:47850-51003	RND efflux pump conferring resistance to fluoroquinolone	diaminopyrimidine, fluoroquinolone, glycylcycline, nitrofuran, tetracycline
contig00137	9040	9906	SHV-187	0/0	100.0	99.5	LN515533:0-867	From the Lahey list of beta-lactamases.	carbapenem, cephalosporin, penam
contig00202	3432	4271	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00122	6184	7044	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00257	860	2106	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00122	5182	6042	(AGly)aac3-IIa	0/0	100	100.0	X51534:91-951	(AGly)aac3-IIa	NA
contig00053	18628	19788	(Bla)ampH	0/0	100	99.9	CP003785:4208384-4209544	(Bla)ampH	NA
contig00122	9866	10741	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00137	9040	9906	(Bla)blaSHV-187	0/0	100	99.5	LN515533:1-867	(Bla)blaSHV-187	NA
contig00122	6184	7044	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00075	12852	13271	(Fcyn)FosA6	0/0	100	99.5	KU254579:59422-59841	(Fcyn)FosA6	NA
contig00017	10037	11212	(Flq)OqxA	0/0	100	99.4	EU370913:46652-47827	(Flq)OqxA	NA
contig00017	6861	10013	(Flq)OqxBgb	0/0	100	99.2	EU370913:47851-51003	(Flq)OqxBgb	NA
contig00233	425	1084	(Phe)catA1	0/0	100	99.8	V00622:244-903	(Phe)catA1	NA
contig00202	3432	4271	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00257	860	2134	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00257	179	829	(Tet)tetR	0/0	100	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00202	4842	5315	(Tmt)dhfr7	0/0	100	100.0	X58425:594-1067	(Tmt)dhfr7	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00122	5182	6042	aac(3)-IIe	0/0	100	100.0	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00122	9866	10741	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00137	9040	9906	blaSHV-187	0/0	100	99.5	NG_050053.1	class A beta-lactamase SHV-187	BETA-LACTAM
contig00122	6184	7044	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00233	425	1084	catA1	0/0	100	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00202	4842	5315	dfrA7	0/0	100	100.0	NG_047737.1	trimethoprim-resistant dihydrofolate reductase DfrA7	TRIMETHOPRIM
contig00075	12852	13271	fosA_gen	0/0	100	99.8	NG_047884.1	FosA family fosfomycin resistance glutathione transferase	FOSFOMYCIN
contig00017	10037	11212	oqxA10	0/0	100	99.8	NG_050418.1	multidrug efflux RND transporter periplasmic adaptor subunit OqxA10	PHENICOL, QUINOLONE
contig00017	6861	10013	oqxB32	0/0	100	100.0	NG_050452.1	multidrug efflux RND transporter permease subunit OqxB32	PHENICOL, QUINOLONE
contig00202	3432	4271	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00257	935	2134	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00122	5182	6042	AAC3	0/0	100.0	100.0	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00010	8294	9487	ACRA	2/3	99.8	97.7	MEG_400	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00053	18628	19788	AMPH	0/0	100.0	99.9	MEG_730	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00247	1749	3572	ASMA	0/0	100.0	99.3	MEG_1179	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00233	414	1084	CATA	0/0	100.0	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00005	22585	23283	CPXAR	0/0	100.0	99.6	MEG_2116	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00005	23280	24653	CPXAR	0/0	100.0	99.1	MEG_2115	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00202	4842	5315	DFRA	0/0	100.0	100.0	MEG_2548	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00075	12852	13271	FOSA	0/0	100.0	99.8	MEG_2993	Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA	NA
contig00048	11011	12243	KDEA	0/0	100.0	100.0	MEG_3447	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:KDEA	NA
contig00067	11440	12939	KMRA	0/0	100.0	99.3	MEG_3460	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:KMRA	NA
contig00113	10340	11512	KPN	0/0	100.0	99.3	MEG_3512	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:KPN	NA
contig00063	3564	3926	KPNE	0/0	100.0	99.2	MEG_3514	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:KPNE	NA
contig00063	3913	4242	KPNF	0/0	100.0	100.0	MEG_3515	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:KPNF	NA
contig00082	19762	20865	KPNO	4/18	99.5	95.3	MEG_3516	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:KPNO	NA
contig00059	13299	14453	OMP37	7/32	99.9	95.2	MEG_4283	Drugs:betalactams:Mutant_porin_proteins:OMP37	NA
contig00017	10037	11212	OQXA	0/0	100.0	99.8	MEG_4326	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:OQXA	NA
contig00017	6861	10013	OQXB	0/0	100.0	100.0	MEG_4339	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:OQXB	NA
contig00021	40562	42028	PHOR	0/0	100.0	99.8	MEG_5786	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_regulator:PHOR	NA
contig00137	9000	10003	SHV	0/0	99.7	98.9	MEG_6428	Drugs:betalactams:Class_A_betalactamases:SHV	NA
contig00202	3305	4272	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00122	6166	7411	TEM	0/0	98.3	99.3	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00257	860	2134	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA

ID098

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00268	1694	2554	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00299	1540	2139	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00137	1442	2230	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00259	1703	2578	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00299	579	1409	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00122	49	909	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00176	223	882	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig00137	838	1311	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00006	41013	42245	mdf(A)_1	0/0	100.0	98.3	Y08743	mdf(A)
contig00515	67	959	mph(A)_1	0/0	98.6	100.0	D16251	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00137	2750	3616	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00208	1712	2958	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline
contig00198	849	2054	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00268	1694	2554	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00299	1540	2139	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00137	1442	2230	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00005	117721	120870	acrB	0/0	100.0	99.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00015	49488	52601	acrD	0/0	100.0	98.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00169	3	1160	acrE	0/0	100.0	98.2	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00169	1172	4276	acrF	0/0	100.0	97.5	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00009	354	1016	acrS	0/0	100.0	97.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00007	688	1507	bacA	0/0	99.8	97.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00173	3080	3801	baeR	0/0	99.9	97.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00173	1680	3083	baeS	0/0	100.0	92.1	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00176	223	882	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00032	15958	16590	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00259	1703	2578	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00137	838	1311	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00020	43734	44906	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00020	44923	46461	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00060	21731	22786	emrK	0/0	100.0	96.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00020	43077	43607	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00060	20193	21731	emrY	0/0	100.0	98.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00037	10125	11768	eptA	0/0	100.0	98.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00005	120893	122086	Escherichia_coli_acrA	0/0	100.0	99.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00062	12898	14031	Escherichia_coli_ampC	0/0	100.0	98.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00015	14955	16259	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	95.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00005	30315	31472	Escherichia_coli_ampH	0/0	100.0	97.3	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00304	1812	2140	Escherichia_coli_emrE	0/0	98.8	91.8	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00006	41013	42245	Escherichia_coli_mdfA	0/0	100.0	96.8	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00060	23309	23923	evgA	0/0	100.0	99.3	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00060	23928	27521	evgS	0/0	100.0	96.6	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00053	8537	9265	gadW	0/0	100.0	95.9	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00053	7344	8168	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00021	1492	1905	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00024	15684	16361	kdpE	0/0	100.0	95.6	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00030	23452	23835	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00372	1	1156	mdtA	0/0	92.6	97.4	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00053	12766	13923	mdtE	0/0	100.0	99.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00053	9628	12741	mdtF	0/0	100.0	98.4	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00023	35049	36275	mdtG	0/0	100.0	98.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00023	25210	26418	mdtH	0/0	100.0	98.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00068	25112	26344	mdtM	0/0	100.0	100.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00170	409	1620	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00026	6570	7601	mdtN	0/0	100.0	97.7	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00026	7601	9652	mdtO	0/0	100.0	96.6	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00026	9649	11115	mdtP	0/0	100.0	96.5	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00515	67	959	mphA	0/0	98.6	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00040	9970	10444	mphB	0/0	99.6	96.2	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00010	26429	28177	msbA	0/0	100.0	98.9	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00299	579	1409	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00019	1874	2842	pmrF	0/0	100.0	97.9	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00137	2777	3616	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00122	49	909	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00208	1712	2958	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00198	849	2054	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00065	22270	23757	tolC	0/0	100.0	97.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00152	1991	3157	ugd	0/0	100.0	96.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00017	29227	30870	yojI	0/0	100.0	97.8	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00268	1694	2554	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00137	1442	2230	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00015	14955	16259	(Bla)AmpC1_Ecoli	0/0	100.0	95.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00062	12898	14031	(Bla)AmpC2_Ecoli	0/0	100.0	98.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00005	30315	31472	(Bla)ampH_Ecoli	0/0	100.0	97.3	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00259	1703	2578	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00299	579	1409	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00122	49	909	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00061	4963	6864	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	98.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00515	67	959	(MLS)mph(A)	0/0	98.6	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00176	223	882	(Phe)catA1	0/0	100.0	99.8	V00622:244-903	(Phe)catA1	NA
contig00137	2777	3616	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00208	1684	2958	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00198	849	2054	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00208	2989	3639	(Tet)tetR	0/0	100.0	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00137	838	1311	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00268	1694	2554	aac(3)-IIe	0/0	100.0	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00299	1540	2094	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00137	1442	2230	aadA5	0/0	100.0	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00259	1703	2578	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00062	12898	14031	blaEC-19	0/0	100.0	99.8	NG_049084.1	class C extended-spectrum beta-lactamase EC-19	CEPHALOSPORIN
contig00299	579	1409	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00122	49	909	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00176	223	882	catA1	0/0	100.0	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00137	838	1311	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00515	67	959	mph(A)	0/0	98.6	100.0	NG_047985.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00137	2777	3616	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00208	1684	2883	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE
contig00198	849	2054	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00268	1694	2554	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00005	120893	122086	ACRA	0/0	100.0	99.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00005	117721	120870	ACRB	0/0	100.0	99.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00015	49488	52601	ACRD	0/0	100.0	98.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00169	3	1160	ACRE	0/0	100.0	98.2	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00169	1172	4276	ACRF	0/0	100.0	97.5	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00009	354	1016	ACRS	0/0	100.0	97.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00005	30315	31472	AMPH	0/0	100.0	97.3	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00137	1442	2230	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00007	688	1507	BACA	0/0	99.8	97.2	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00173	3080	3801	BAER	0/0	99.9	97.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00173	1680	3083	BAES	0/0	100.0	92.1	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00017	2764	3954	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00062	12898	14031	BLAEC	0/0	100.0	99.8	MEG_1277	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00176	212	882	CATA	0/0	100.0	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00236	1264	1962	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00032	15958	16590	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00259	1454	2682	CTX	0/0	100.0	99.9	MEG_2393	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00137	838	1311	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00020	43734	44906	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00020	44923	46461	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00057	18757	19947	EMRD	0/0	100.0	97.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00060	21731	22894	EMRK	0/0	100.0	96.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00020	43077	43607	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00060	20193	21731	EMRY	0/0	100.0	98.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00037	10125	11768	EPTA	0/0	100.0	98.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00060	23928	27521	EVGS	0/0	100.0	97.1	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00053	8537	9265	GADW	0/0	100.0	97.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00053	7344	8168	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00021	1492	1905	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00024	15684	16361	KDPE	0/0	100.0	95.6	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00030	23446	23835	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00030	22997	23431	MARR	0/0	100.0	98.6	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00006	41013	42245	MDFA	0/0	100.0	98.4	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00372	1	1156	MDTA	0/0	92.6	97.4	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00053	12766	13923	MDTE	0/0	100.0	99.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00053	9628	12741	MDTF	0/0	100.0	98.4	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00023	35049	36275	MDTG	0/0	100.0	98.7	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00023	25210	26418	MDTH	0/0	100.0	98.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00004	127847	128176	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00004	127495	127860	MDTJ	0/0	100.0	98.6	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00004	60494	61866	MDTK	0/0	99.9	97.9	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00068	25112	26344	MDTM	0/0	100.0	100.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00170	409	1620	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00026	6570	7601	MDTN	0/0	100.0	97.7	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00026	7601	9652	MDTO	0/0	100.0	96.6	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00026	9649	11115	MDTP	0/0	100.0	96.5	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00515	67	959	MPHA	0/0	98.6	100.0	MEG_4029	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00040	9970	10444	MPHB	0/0	99.6	96.2	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00010	26429	28177	MSBA	0/0	100.0	98.9	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00304	1812	2140	MVRC	0/0	98.8	91.8	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00299	579	1409	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00061	4963	6864	PBP2	0/0	100.0	98.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00015	14955	16259	PBP4B	0/0	100.0	95.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00019	1874	2842	PMRF	0/0	100.0	97.9	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00026	31316	31638	SOXS	0/0	99.7	97.8	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00137	2776	3743	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00208	1684	2958	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00198	849	2054	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00152	1991	3157	UGD	0/0	100.0	96.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00017	29227	30870	YOGI	0/0	100.0	97.8	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID099

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00110	137	925	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00013	67769	68644	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00075	8178	9038	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00107	182	664	dfrA14_5	0/0	100	99.6	DQ388123	dfrA14	Trimethoprim
contig00110	1056	1529	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00003	102470	103702	mdf(A)_1	0/0	100	99.0	Y08743	mdf(A)
contig00075	2160	2816	qnrS1_1	0/0	100	100.0	AB187515	qnrS1	Ciprofloxacin
contig00088	3459	4274	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole
contig00075	9296	10087	sul3_2	0/0	100	100.0	AJ459418	sul3	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00110	137	925	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00014	38756	41905	acrB	0/0	100.0	99.5	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00002	135389	138502	acrD	0/0	100.0	99.3	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00016	65943	66764	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00007	128547	129269	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00007	127147	128550	baeS	0/0	100.0	99.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00020	7847	9220	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00009	176	808	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00013	67769	68644	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00107	182	664	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00110	1056	1529	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00015	23952	25124	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00015	25141	26679	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00006	10434	11489	emrK	0/0	100.0	99.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00015	23295	23825	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00006	11489	13027	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00024	7727	9370	eptA	0/0	100.0	99.5	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00014	37540	38733	Escherichia_coli_acrA	0/0	100.0	99.5	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00024	51583	52716	Escherichia_coli_ampC	0/0	100.0	97.4	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00002	169833	171137	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.7	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00059	15203	16360	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00003	102470	103702	Escherichia_coli_mdfA	0/0	100.0	97.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00006	9296	9910	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00006	5698	9291	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00038	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00038	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00087	938	1351	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00023	8068	8745	kdpE	0/0	100.0	99.4	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00027	44430	44813	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00007	118287	119534	mdtA	0/0	100.0	100.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00007	119534	122656	mdtB	0/0	100.0	98.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00007	122657	125734	mdtC	0/0	100.0	99.8	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00038	6013	7170	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00038	2875	5988	mdtF	0/0	100.0	99.9	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00001	138913	140139	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00001	148768	149976	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00072	465	1676	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00019	71052	72083	mdtN	0/0	100.0	99.5	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00019	69001	71052	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00019	67538	69004	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00002	114229	114705	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	2196	3944	msbA	0/0	100.0	99.9	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00006	110978	111946	pmrF	0/0	100.0	99.9	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00075	2160	2816	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00088	3459	4274	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00075	9296	10087	sul3	0/0	100.0	100.0	FJ196385:9323-8531	Sul3 is a sulfonamide resistant dihydropteroate synthase similar to Sul1 and Sul2. Its resistance gene was found encoded in E. coli plasmid DNA of sulfonamide resistant isolates.	sulfonamide
contig00075	8178	9038	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00016	42080	43567	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00051	22605	24248	yojI	0/0	100.0	99.9	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00110	137	925	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00002	169833	171137	(Bla)AmpC1_Ecoli	0/0	100	98.7	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00024	51583	52716	(Bla)AmpC2_Ecoli	0/0	100	97.4	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00059	15203	16360	(Bla)ampH_Ecoli	0/0	100	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00013	67769	68644	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00075	8178	9038	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00023	60539	62440	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00075	2160	2816	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00088	3459	4274	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00075	9296	10087	(Sul)sul3	0/0	100	100.0	HQ875016:7396-8187	(Sul)sul3	NA
contig00114	172	822	(Tet)tetR	0/0	100	99.8	HF545434:53576-54226	(Tet)tetR	NA
contig00107	182	655	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA
contig00110	1056	1529	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00110	137	925	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00013	67769	68644	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00024	51583	52716	blaEC	0/0	100	98.2	NG_047496.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00075	8178	9038	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00107	182	655	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00110	1056	1529	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00075	2160	2816	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00088	3459	4274	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00075	9296	10087	sul3	0/0	100	100.0	NG_048120.1	sulfonamide-resistant dihydropteroate synthase Sul3	SULFONAMIDE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00014	37540	38733	ACRA	0/0	100.0	99.5	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00014	38756	41905	ACRB	0/0	100.0	99.5	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00002	135389	138502	ACRD	0/0	100.0	99.3	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00059	15203	16360	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00110	137	925	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00007	104022	105874	ASMA	0/0	100.0	98.0	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00016	65943	66764	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00007	128547	129269	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00007	127147	128550	BAES	0/0	100.0	99.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00042	14113	15303	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00024	51583	52716	BLAEC	0/0	100.0	98.2	MEG_1276	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00020	7152	7850	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00020	7847	9220	CPXAR	0/0	100.0	99.4	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	176	808	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00095	329	1217	CTX	0/0	100.0	95.4	MEG_2430	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00095	2404	3262	CTX	0/0	96.6	99.7	MEG_2430	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00107	182	655	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00110	1056	1529	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00015	23952	25124	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00015	25141	26679	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00017	16747	17937	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00006	10326	11489	EMRK	0/0	100.0	99.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00015	23295	23825	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00006	11489	13027	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00024	7727	9370	EPTA	0/0	100.0	99.5	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00006	5698	9291	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00038	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00038	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00087	938	1351	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00023	8068	8745	KDPE	0/0	100.0	99.4	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00027	44424	44813	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00027	43976	44410	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00003	102470	103702	MDFA	0/0	100.0	99.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00007	118287	119534	MDTA	0/0	100.0	100.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00007	119534	122656	MDTB	0/0	100.0	98.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00007	122657	125734	MDTC	0/0	100.0	99.8	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00038	6013	7170	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00038	2875	5988	MDTF	0/0	100.0	99.9	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00001	138913	140139	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00001	148768	149976	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00011	115559	115888	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00011	115207	115572	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00011	43747	45120	MDTK	0/0	100.0	98.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00072	465	1676	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00019	71052	72083	MDTN	0/0	100.0	99.5	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00019	69001	71052	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00019	67538	69004	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00002	114229	114705	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	2196	3944	MSBA	0/0	100.0	99.9	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00023	60539	62440	PBP2	0/0	100.0	99.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00002	169833	171137	PBP4B	0/0	100.0	98.7	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00006	110978	111946	PMRF	0/0	100.0	99.9	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00075	2160	2816	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00026	21725	22594	ROBA	0/0	100.0	98.8	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00019	45260	45582	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00088	3459	4274	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00075	9296	10087	SULIII	0/0	100.0	100.0	MEG_6639	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULIII	NA
contig00075	7811	9056	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00051	22605	24248	YOGI	0/0	100.0	99.9	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID24

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00061	2721	3522	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00085	1684	2559	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00061	1826	2323	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00088	266	1029	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00002	84130	85362	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00061	10161	11091	mph(A)_2	2/10	100.0	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00061	4000	4866	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00083	850	2055	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00061	2743	3522	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00001	99712	102861	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00009	135351	138464	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00011	127888	129045	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00011	129057	132161	acrF	0/0	100.0	99.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00011	126827	127489	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	90602	91423	bacA	0/0	100.0	99.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00041	29821	30543	baeR	0/0	100.0	99.6	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00041	28421	29824	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00013	61323	62696	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00010	15201	15833	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00085	1684	2559	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00061	1826	2323	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00007	90366	91538	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00007	91555	93093	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00023	1067	2122	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00007	89709	90239	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00030	7740	9383	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00088	292	1037	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00001	98496	99689	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	107745	108878	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00023	65523	66827	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00001	187826	188983	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00002	84130	85362	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00023	2646	3260	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00023	3265	6858	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00036	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00036	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00004	91674	92087	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00024	8166	8843	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00042	31344	31727	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00041	19561	20808	mdtA	0/0	100.0	97.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00041	20808	23930	mdtB	0/0	100.0	99.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00041	23931	27008	mdtC	0/0	100.0	99.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00036	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00036	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00032	18401	19627	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00032	28256	29464	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00048	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00015	21771	22802	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00015	22802	24853	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00015	24850	26316	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00061	10189	11091	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00009	114189	114665	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00002	167077	168825	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00003	173789	174757	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00061	4027	4866	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00083	850	2055	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00008	66737	68224	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00003	113686	115329	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00061	2743	3522	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00023	65523	66827	(Bla)AmpC1_Ecoli	0/0	100.0	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00006	107745	108878	(Bla)AmpC2_Ecoli	0/0	100.0	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00001	187826	188983	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00085	1684	2559	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00024	60253	62154	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00088	292	1029	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00061	10189	11091	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00061	4027	4866	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00083	850	2055	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00061	1826	2323	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00061	2731	3522	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00085	1684	2559	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00006	107745	108878	blaEC	0/0	100	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00061	1826	2323	dfrA12	0/0	100	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00088	292	1029	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00061	10161	11091	mph(A)	2/10	100	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00061	4027	4866	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00083	850	2055	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00001	98496	99689	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00001	99712	102861	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00009	135351	138464	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00011	127888	129045	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00011	129057	132161	ACRF	0/0	100.0	99.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00011	126827	127489	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00006	107745	108878	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00001	187826	188983	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00061	2721	3522	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00041	5770	7622	ASMA	0/0	100.0	97.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00008	90602	91423	BACA	0/0	100.0	99.9	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00041	29821	30543	BAER	0/0	100.0	99.6	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00041	28421	29824	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00003	86709	87899	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00013	60628	61326	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00013	61323	62696	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00010	15201	15833	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00106	61	984	CTX	0/0	98.0	98.3	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00061	1826	2323	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00007	90366	91538	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00007	91555	93093	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00012	87171	88361	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00023	1067	2230	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00007	89709	90239	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00030	7740	9383	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00088	266	1029	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00023	3265	6858	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00036	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00036	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00004	91674	92087	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00024	8166	8843	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00042	31338	31727	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00042	30890	31324	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00002	84130	85362	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00041	19561	20808	MDTA	0/0	100.0	97.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00041	20808	23930	MDTB	0/0	100.0	99.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00041	23931	27008	MDTC	0/0	100.0	99.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00036	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00036	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00032	18401	19627	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00032	28256	29464	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00039	1757	2086	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00039	2073	2438	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00026	31959	33332	MDTK	0/0	100.0	98.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00048	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00015	21771	22802	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00015	22802	24853	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00015	24850	26316	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00061	10161	11091	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00009	114189	114665	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00002	167077	168825	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00024	60253	62154	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00023	65523	66827	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00003	173789	174757	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00005	38665	39534	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00015	47933	48256	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00061	4026	4993	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00083	850	2055	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00003	113686	115329	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

Summary figures

Presence/Absence of antibiotic resistance genes (coverage and identity > 90%) on each sample

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Plasmid Profiling

Field	Description
Contig	Contig name where the gene was found
Start	Start position of the gene within the contig
End	End position of the gene within the contig
Gene	Antibiotic resistance gene
Gaps	Gaps in subject (genome) and query (antibiotic resistance gene)
Coverage	Proportion (%) of the gene covered
Identity	Proportion (%) of exact nucleotide matches
Accession	Accesion number of the antibiotic resistance gene
Product	Antibiotic resistance gene product

Select sample

ID005zero

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00052	400	632	Col(BS512)_1	0/0	100.0	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00037	3630	3771	Col156_1	0/0	92.2	98.6	NC_009781	Col156_1__NC_009781
contig00044	3338	3491	Col156_1	0/0	100.0	94.8	NC_009781	Col156_1__NC_009781
contig00031	14320	14707	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00033	14397	15078	IncFIB(AP001918)_1	0/0	100.0	96.6	AP001918	IncFIB(AP001918)_1__AP001918

ID008

## [1] "NO PLASMID FOUND!!"

ID009

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00073	13248	13807	IncFIB(K)_1_Kpn3	0/0	100	98.8	JN233704	IncFIB(K)_1_Kpn3_JN233704
contig00039	16038	16776	IncL/M(pMU407)_1_pMU407	0/0	100	99.5	U27345	IncL/M(pMU407)_1_pMU407_U27345

ID011

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00230	459	613	IncB/O/K/Z_2	1/1	96.2	95.5	GU256641	IncB/O/K/Z_2__GU256641
contig00288	462	613	IncB/O/K/Z_3	0/0	100.0	99.3	GQ259888	IncB/O/K/Z_3__GQ259888

ID013

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00025	12158	12545	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00309	1833	2514	IncFIB(AP001918)_1	0/0	100.0	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00413	3304	3553	IncFII_1	0/0	95.8	100.0	AY458016	IncFII_1__AY458016

ID014at24

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00065	1438	1579	Col156_1	0/0	92.2	98.6	NC_009781	Col156_1__NC_009781
contig00253	4077	4230	Col156_1	0/0	100.0	94.8	NC_009781	Col156_1__NC_009781
contig00381	414	620	Col8282_1	0/0	100.0	100.0	DQ995352	Col8282_1__DQ995352
contig01853	681	1068	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00043	8903	9584	IncFIB(AP001918)_1	0/0	100.0	96.9	AP001918	IncFIB(AP001918)_1__AP001918
contig00003	7323	7696	IncX1_1	0/0	100.0	98.4	EU370913	IncX1_1__EU370913

ID015HW

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00101	433	694	Col(MG828)_1	0/0	100	92.8	NC_008486	Col(MG828)_1__NC_008486
contig00045	3365	3752	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00045	26541	27222	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00062	3328	3588	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5	0/0	100	98.1	CP024805.1	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5_CP024805.1

ID015at48

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00115	433	694	Col(MG828)_1	0/0	100	92.8	NC_008486	Col(MG828)_1__NC_008486
contig00073	9286	9673	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00074	8768	9449	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00070	3328	3588	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5	0/0	100	98.1	CP024805.1	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5_CP024805.1

ID016at24

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00070	14298	14685	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00097	1569	2250	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00094	3324	3584	IncFII_1	0/0	100	100.0	AY458016	IncFII_1__AY458016
contig00061	13995	14136	IncI1_1_Alpha	0/0	100	97.9	AP005147	IncI1_1_Alpha_AP005147

ID017at48

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00211	4	114	Col440I_1	0/0	97.4	92.8	CP023920.1	Col440I_1__CP023920.1
contig00092	14297	14684	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00144	1833	2514	IncFIB(AP001918)_1	0/0	100.0	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00091	3323	3583	IncFII_1	0/0	100.0	100.0	AY458016	IncFII_1__AY458016
contig00096	1715	1856	IncI1_1_Alpha	0/0	100.0	97.9	AP005147	IncI1_1_Alpha_AP005147

ID018at24

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00067	3630	3771	Col156_1	0/0	92.2	98.6	NC_009781	Col156_1__NC_009781
contig00077	3338	3491	Col156_1	0/0	100.0	94.8	NC_009781	Col156_1__NC_009781
contig00062	10944	11331	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00059	14397	15078	IncFIB(AP001918)_1	0/0	100.0	96.6	AP001918	IncFIB(AP001918)_1__AP001918

ID020at24

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00105	366	476	Col440I_1	0/0	97.4	93.7	CP023920.1	Col440I_1__CP023920.1
contig00031	4855	5115	IncFII(pCoo)_1_pCoo	1/1	99.6	96.6	CR942285	IncFII(pCoo)_1_pCoo_CR942285
contig00054	24232	24605	IncX2_1	0/0	100.0	100.0	JQ269335	IncX2_1__JQ269335
contig00078	1713	2477	IncY_1	0/0	100.0	99.5	K02380	IncY_1__K02380

ID021at24

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00131	428	686	Col(MG828)_1	1/1	98.8	95.0	NC_008486	Col(MG828)_1__NC_008486
contig00106	4075	4228	Col156_1	0/0	100.0	94.8	NC_009781	Col156_1__NC_009781
contig00110	414	620	Col8282_1	0/0	100.0	100.0	DQ995352	Col8282_1__DQ995352
contig00111	1730	1860	ColRNAI_1	1/1	100.0	90.1	DQ298019	ColRNAI_1__DQ298019
contig00064	6481	6640	IncB/O/K/Z_2	0/0	100.0	100.0	GU256641	IncB/O/K/Z_2__GU256641
contig00102	1412	1672	IncFII_1	0/0	100.0	100.0	AY458016	IncFII_1__AY458016

ID025III

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00807	789	1176	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00322	1	616	IncFIB(AP001918)_1	0/0	90.3	98.5	AP001918	IncFIB(AP001918)_1__AP001918
contig00530	768	909	IncI1_1_Alpha	0/0	100.0	97.9	AP005147	IncI1_1_Alpha_AP005147

ID025II

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00072	14298	14685	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00095	1417	2098	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00044	38031	38291	IncFII_1	0/0	100	100.0	AY458016	IncFII_1__AY458016
contig00057	15823	15964	IncI1_1_Alpha	0/0	100	97.9	AP005147	IncI1_1_Alpha_AP005147

ID025I

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00058	14298	14685	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00081	1833	2514	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00038	38031	38291	IncFII_1	0/0	100	100.0	AY458016	IncFII_1__AY458016
contig00048	16406	16547	IncI1_1_Alpha	0/0	100	97.9	AP005147	IncI1_1_Alpha_AP005147

ID026

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00090	1088	1198	Col440I_1	0/0	97.4	92.8	CP023920.1	Col440I_1__CP023920.1
contig00056	14298	14685	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00075	1833	2514	IncFIB(AP001918)_1	0/0	100.0	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00039	38451	38711	IncFII_1	0/0	100.0	100.0	AY458016	IncFII_1__AY458016
contig00054	12304	12445	IncI1_1_Alpha	0/0	100.0	97.9	AP005147	IncI1_1_Alpha_AP005147

ID027

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00062	14298	14685	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00081	1833	2514	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00040	38031	38291	IncFII_1	0/0	100	100.0	AY458016	IncFII_1__AY458016
contig00052	15823	15964	IncI1_1_Alpha	0/0	100	97.9	AP005147	IncI1_1_Alpha_AP005147

ID031

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00072	433	694	Col(MG828)_1	0/0	100.0	93.1	NC_008486	Col(MG828)_1__NC_008486
contig00037	5825	5979	IncB/O/K/Z_2	1/1	96.2	96.1	GU256641	IncB/O/K/Z_2__GU256641
contig00049	1436	2117	IncFIB(AP001918)_1	0/0	100.0	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00031	7275	7648	IncX1_1	0/0	100.0	98.4	EU370913	IncX1_1__EU370913

ID032I

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00079	433	694	Col(MG828)_1	0/0	100	93.5	NC_008486	Col(MG828)_1__NC_008486
contig00063	4077	4230	Col156_1	0/0	100	94.8	NC_009781	Col156_1__NC_009781
contig00042	16297	16684	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00042	5009	5690	IncFIB(AP001918)_1	0/0	100	99.7	AP001918	IncFIB(AP001918)_1__AP001918

ID033I

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00068	1039	1923	p0111_1	0/0	100	98.6	AP010962	p0111_1__AP010962

ID034II

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00055	14298	14685	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00078	1833	2514	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00035	41580	41840	IncFII_1	0/0	100	100.0	AY458016	IncFII_1__AY458016
contig00046	15823	15964	IncI1_1_Alpha	0/0	100	97.9	AP005147	IncI1_1_Alpha_AP005147

ID034I

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00100	1088	1198	Col440I_1	0/0	97.4	92.8	CP023920.1	Col440I_1__CP023920.1
contig00061	14298	14685	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00083	1833	2514	IncFIB(AP001918)_1	0/0	100.0	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00040	38031	38291	IncFII_1	0/0	100.0	100.0	AY458016	IncFII_1__AY458016
contig00071	57	198	IncI1_1_Alpha	0/0	100.0	97.9	AP005147	IncI1_1_Alpha_AP005147

ID037

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00112	519	632	Col440I_1	0/0	100	90.3	CP023920.1	Col440I_1__CP023920.1
contig00113	155	268	Col440I_1	0/0	100	91.2	CP023920.1	Col440I_1__CP023920.1
contig00105	255	768	IncN_1	0/0	100	99.8	AY046276	IncN_1__AY046276

ID043I

## [1] "NO PLASMID FOUND!!"

ID045

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00024	56680	56832	IncB/O/K/Z_2	1/1	95	96.1	GU256641	IncB/O/K/Z_2__GU256641
contig00049	5210	5891	IncFIB(AP001918)_1	0/0	100	97.8	AP001918	IncFIB(AP001918)_1__AP001918
contig00069	278	791	IncN_1	0/0	100	100.0	AY046276	IncN_1__AY046276
contig00062	9173	9546	IncX2_1	0/0	100	99.7	JQ269335	IncX2_1__JQ269335

ID047

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00114	400	632	Col(BS512)_1	0/0	100.0	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00120	429	690	Col(MG828)_1	0/0	100.0	91.6	NC_008486	Col(MG828)_1__NC_008486
contig00072	3584	3725	Col156_1	0/0	92.2	98.6	NC_009781	Col156_1__NC_009781
contig00046	19761	20148	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00046	8473	9154	IncFIB(AP001918)_1	0/0	100.0	99.7	AP001918	IncFIB(AP001918)_1__AP001918
contig00033	41587	41847	IncFII(pRSB107)_1_pRSB107	0/0	100.0	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089

ID050

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00082	4078	4231	Col156_1	0/0	100	94.8	NC_009781	Col156_1__NC_009781
contig00057	9159	9542	IncFIA_1	0/0	99	99.7	AP001918	IncFIA_1__AP001918
contig00064	8464	9145	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918

ID051

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00041	6604	6757	Col156_1	0/0	100	98.7	NC_009781	Col156_1__NC_009781
contig00139	3382	4063	IncFIB(AP001918)_1	0/0	100	96.6	AP001918	IncFIB(AP001918)_1__AP001918
contig00006	17801	18443	IncFIB(pB171)_1_pB171	0/0	100	99.2	AB024946	IncFIB(pB171)_1_pB171_AB024946
contig00007	5323	5696	IncX1_1	0/0	100	98.9	EU370913	IncX1_1__EU370913

ID052

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00052	16919	17561	IncFIB(pB171)_1_pB171	0/0	100	99.4	AB024946	IncFIB(pB171)_1_pB171_AB024946
contig00064	18329	18589	IncFII(pRSB107)_1_pRSB107	0/0	100	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089

ID057

## [1] "NO PLASMID FOUND!!"

ID058

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00069	4081	4845	IncY_1	0/0	100	98.8	K02380	IncY_1__K02380
contig00085	2535	3419	p0111_1	0/0	100	98.6	AP010962	p0111_1__AP010962

ID066

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00072	400	632	Col(BS512)_1	0/0	100.0	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00058	4076	4229	Col156_1	0/0	100.0	94.8	NC_009781	Col156_1__NC_009781
contig00048	3426	3813	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00050	6524	7205	IncFIB(AP001918)_1	0/0	100.0	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00068	3322	3557	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5	0/0	90.4	97.9	CP024805.1	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5_CP024805.1
contig00046	12575	12948	IncX1_1	0/0	100.0	94.9	EU370913	IncX1_1__EU370913

ID070

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00128	431	692	Col(MG828)_1	0/0	100.0	92.8	NC_008486	Col(MG828)_1__NC_008486
contig00075	11383	11493	Col440I_1	0/0	97.4	92.8	CP023920.1	Col440I_1__CP023920.1
contig00070	9148	9531	IncFIA_1	0/0	99.0	99.7	AP001918	IncFIA_1__AP001918
contig00105	1834	2515	IncFIB(AP001918)_1	0/0	100.0	98.4	AP001918	IncFIB(AP001918)_1__AP001918

ID073

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00167	428	686	Col(MG828)_1	1/1	98.8	95	NC_008486	Col(MG828)_1__NC_008486

ID081

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00092	4077	4230	Col156_1	0/0	100	94.8	NC_009781	Col156_1__NC_009781
contig00071	9148	9531	IncFIA_1	0/0	99	99.7	AP001918	IncFIA_1__AP001918
contig00074	8463	9144	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00055	1279	1990	IncX4_2	0/0	100	99.0	FN543504	IncX4_2__FN543504

ID096I

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00185	3435	3994	IncFIB(K)_1_Kpn3	0/0	100	100	JN233704	IncFIB(K)_1_Kpn3_JN233704

ID098

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00307	400	632	Col(BS512)_1	0/0	100	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00183	3981	4111	ColRNAI_1	1/1	100	90.1	DQ298019	ColRNAI_1__DQ298019
contig00124	10533	10920	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00199	1834	2515	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00204	204	464	IncFII(pRSB107)_1_pRSB107	0/0	100	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089

ID099

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00085	4314	4687	IncX1_1	0/0	100	98.7	EU370913	IncX1_1__EU370913

ID24

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00081	1088	1198	Col440I_1	0/0	97.4	92.8	CP023920.1	Col440I_1__CP023920.1
contig00049	14298	14685	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00069	1833	2514	IncFIB(AP001918)_1	0/0	100.0	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00034	38031	38291	IncFII_1	0/0	100.0	100.0	AY458016	IncFII_1__AY458016
contig00044	15823	15964	IncI1_1_Alpha	0/0	100.0	97.9	AP005147	IncI1_1_Alpha_AP005147

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Virulence Factor Determination

Field	Description
Contig	Contig name where the gene was found
Start	Start position of the gene within the contig
End	End position of the gene within the contig
Gene	Antibiotic resistance gene
Coverage	Proportion (%) of the gene covered
Identity	Proportion (%) of exact nucleotide matches
Accession	Accesion number of the antibiotic resistance gene
Product	Antibiotic resistance gene product

Select the sample

ID005zero

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00020	74873	76301	+	aslA	100.0	98.5	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00006	177711	179657	-	chuA	100.0	99.7	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	176634	177662	-	chuS	100.0	99.5	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	180299	181291	+	chuT	100.0	99.7	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	183827	184819	+	chuU	100.0	99.5	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	184786	185586	+	chuV	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	181311	182648	+	chuW	100.0	99.1	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	182661	183155	+	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	183155	183778	+	chuY	100.0	98.4	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00007	138927	139382	+	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	137524	138174	-	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	136689	137105	-	csgF	99.0	80.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	135829	136662	-	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	289871	290617	-	entA	100.0	98.4	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	290617	291474	-	entB	100.0	99.2	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	293108	294295	-	entC	100.0	99.7	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	308753	309414	+	entD	85.9	92.8	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	291488	293098	-	entE	100.0	99.1	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	300972	304825	-	entF	99.3	98.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	295432	296682	-	entS	100.0	98.8	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00013	22805	27055	-	fdeC	100.0	99.6	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00003	306488	308728	+	fepA	100.0	98.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	294472	295428	+	fepB	100.0	99.8	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	298783	299598	+	fepC	100.0	99.4	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	296781	297797	+	fepD	100.0	99.5	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	297794	298786	+	fepG	100.0	99.8	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	305043	306245	-	fes	100.0	99.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00002	319718	320323	-	fimA	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	321822	322424	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	318352	319077	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	315649	318285	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	320748	321344	-	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	315109	315642	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	314593	315096	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	313671	314582	-	fimH	100.0	97.2	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	319114	319653	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00001	512185	514206	-	fyuA	100.0	100.0	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00008	187741	188571	+	gspC	100.0	93.9	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	188811	190661	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	190661	192154	+	gspE	100.0	94.9	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	192154	193353	+	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	193394	193849	+	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	193886	194416	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	194413	194784	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	194817	195386	+	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	195383	196360	+	gspK	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	196675	197535	+	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	197651	198072	+	gspM	99.8	93.6	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	517815	527306	-	irp1	100.0	99.3	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	527396	533500	-	irp2	100.0	98.9	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00028	10165	11946	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00028	11947	12894	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00028	12894	14636	+	iucC	100.0	98.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00028	14633	15954	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00028	15892	18193	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00008	211226	212902	-	kpsD	100.0	99.0	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00008	199132	199908	+	kpsM	100.0	99.9	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00008	199905	200564	+	kpsT	100.0	100.0	AAA24047	(kpsT) KpsT [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00007	67818	68858	-	ompA	100.0	99.5	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00028	747	1060	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00028	1465	1698	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00059	256	807	+	papX	100.0	97.5	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00028	19128	23028	+	sat	100.0	99.5	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00037	8438	9576	+	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00013	46763	50895	+	vat	100.0	99.7	NP_752330	(vat) Haemoglobin protease [Tsh (VF0233)] [Escherichia coli CFT073]
contig00013	42393	43146	+	yagV/ecpE	99.7	98.4	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	40826	42469	+	yagW/ecpD	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	38311	40836	+	yagX/ecpC	100.0	97.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	37617	38285	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	36973	37560	+	yagZ/ecpA	100.0	98.5	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	533691	534650	-	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	514337	515914	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	534817	536619	+	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	536606	538408	+	ybtQ	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	539709	541013	+	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	515918	516721	-	ybtT	100.0	99.5	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	516718	517818	-	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	538401	539681	+	ybtX	100.0	99.6	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00013	36308	36898	+	ykgK/ecpR	100.0	99.3	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID008

## Error in read.table("ID008_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00020	74873	76301	+	aslA	100.0	98.5	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00006	177711	179657	-	chuA	100.0	99.7	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	176634	177662	-	chuS	100.0	99.5	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	180299	181291	+	chuT	100.0	99.7	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	183827	184819	+	chuU	100.0	99.5	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	184786	185586	+	chuV	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	181311	182648	+	chuW	100.0	99.1	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	182661	183155	+	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	183155	183778	+	chuY	100.0	98.4	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00007	138927	139382	+	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	137524	138174	-	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	136689	137105	-	csgF	99.0	80.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	135829	136662	-	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	289871	290617	-	entA	100.0	98.4	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	290617	291474	-	entB	100.0	99.2	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	293108	294295	-	entC	100.0	99.7	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	308753	309414	+	entD	85.9	92.8	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	291488	293098	-	entE	100.0	99.1	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	300972	304825	-	entF	99.3	98.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	295432	296682	-	entS	100.0	98.8	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00013	22805	27055	-	fdeC	100.0	99.6	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00003	306488	308728	+	fepA	100.0	98.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	294472	295428	+	fepB	100.0	99.8	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	298783	299598	+	fepC	100.0	99.4	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	296781	297797	+	fepD	100.0	99.5	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	297794	298786	+	fepG	100.0	99.8	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	305043	306245	-	fes	100.0	99.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00002	319718	320323	-	fimA	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	321822	322424	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	318352	319077	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	315649	318285	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	320748	321344	-	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	315109	315642	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	314593	315096	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	313671	314582	-	fimH	100.0	97.2	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	319114	319653	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00001	512185	514206	-	fyuA	100.0	100.0	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00008	187741	188571	+	gspC	100.0	93.9	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	188811	190661	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	190661	192154	+	gspE	100.0	94.9	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	192154	193353	+	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	193394	193849	+	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	193886	194416	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	194413	194784	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	194817	195386	+	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	195383	196360	+	gspK	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	196675	197535	+	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	197651	198072	+	gspM	99.8	93.6	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	517815	527306	-	irp1	100.0	99.3	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	527396	533500	-	irp2	100.0	98.9	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00028	10165	11946	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00028	11947	12894	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00028	12894	14636	+	iucC	100.0	98.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00028	14633	15954	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00028	15892	18193	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00008	211226	212902	-	kpsD	100.0	99.0	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00008	199132	199908	+	kpsM	100.0	99.9	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00008	199905	200564	+	kpsT	100.0	100.0	AAA24047	(kpsT) KpsT [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00007	67818	68858	-	ompA	100.0	99.5	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00028	747	1060	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00028	1465	1698	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00059	256	807	+	papX	100.0	97.5	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00028	19128	23028	+	sat	100.0	99.5	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00037	8438	9576	+	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00013	46763	50895	+	vat	100.0	99.7	NP_752330	(vat) Haemoglobin protease [Tsh (VF0233)] [Escherichia coli CFT073]
contig00013	42393	43146	+	yagV/ecpE	99.7	98.4	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	40826	42469	+	yagW/ecpD	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	38311	40836	+	yagX/ecpC	100.0	97.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	37617	38285	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	36973	37560	+	yagZ/ecpA	100.0	98.5	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	533691	534650	-	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	514337	515914	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	534817	536619	+	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	536606	538408	+	ybtQ	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	539709	541013	+	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	515918	516721	-	ybtT	100.0	99.5	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	516718	517818	-	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	538401	539681	+	ybtX	100.0	99.6	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00013	36308	36898	+	ykgK/ecpR	100.0	99.3	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID009

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00214	5276	6021	-	entA	99.6	80.3	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00214	6031	6882	-	entB	99.3	82.0	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00435	165	936	+	fepC	94.6	80.0	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00018	17974	19044	-	ompA	100.0	83.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00134	274	1027	-	yagV/ecpE	99.7	84.3	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00134	953	2596	-	yagW/ecpD	100.0	88.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00134	2586	5111	-	yagX/ecpC	100.0	87.0	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00134	5137	5805	-	yagY/ecpB	100.0	87.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00134	5867	6450	-	yagZ/ecpA	99.3	90.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00134	6524	7104	-	ykgK/ecpR	98.3	86.9	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID011

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00011	49319	50747	+	aslA	100.0	92.9	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00052	8086	8541	+	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00052	6681	7331	-	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00052	5846	6262	-	csgF	99.0	81.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00052	4986	5819	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00060	8729	9475	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00060	9475	10332	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00060	11966	13153	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00060	27797	28567	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00060	10346	11956	-	entE	100.0	95.4	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00060	20016	23869	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00060	14476	15726	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003	8	1906	-	espL1	100.0	97.5	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	103094	105279	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00074	6773	7827	+	espR1	83.7	93.9	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	144243	145663	+	espX1	99.9	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	73298	74878	-	espX4	100.0	96.5	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	42482	43774	+	espX5	100.0	96.6	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	105181	105977	-	espY1	99.9	88.6	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00096	4096	8344	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00060	25532	27772	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00060	13516	14472	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00060	17827	18642	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00060	15825	16841	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00060	16838	17830	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00060	24087	25289	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00130	2762	3373	-	fimA	100.0	88.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00081	263	865	-	fimB	100.0	97.7	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00130	1396	2121	-	fimC	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00130	3800	4394	-	fimE	99.7	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00070	20536	21069	-	fimF	100.0	97.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00070	20020	20523	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00070	19098	20009	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00130	2158	2697	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00068	7493	9274	-	iucA	100.0	99.9	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00068	6545	7492	-	iucB	100.0	99.9	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00068	4803	6545	-	iucC	100.0	99.9	NP_709456	(iucC) aerobactin synthesis protein IucC [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00068	3469	4806	-	iucD	100.0	99.8	NP_709457	(iucD) aerobactin synthesis protein IucC lysine 6-monooxygenase [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00068	1268	3547	-	iutA	100.0	99.6	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00010	74099	75139	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00096	12030	12617	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00096	11365	11955	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID013

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00394	1991	3419	+	aslA	100.0	97.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00072	780	1808	-	chuS	100.0	97.8	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00072	4445	5437	+	chuT	100.0	98.5	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00072	7973	8965	+	chuU	100.0	99.3	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00072	8932	9732	+	chuV	100.0	99.6	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00072	5457	6794	+	chuW	100.0	98.1	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00072	7301	7924	+	chuY	100.0	97.9	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00972	995	1450	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00414	598	1248	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00414	1667	2083	+	csgF	99.0	81.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00414	2110	2943	+	csgG	100.0	82.7	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00082	3489	4235	+	entA	100.0	96.5	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00082	2632	3489	+	entB	100.0	98.7	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00082	1	998	+	entC	84.0	97.0	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	3909	4679	-	entD	100.0	94.3	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01564	212	881	-	entD	86.9	94.8	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00082	1008	2618	+	entE	100.0	98.6	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	8607	12460	+	entF	99.3	97.3	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00551	1305	2555	-	entS	100.0	95.8	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00101	6057	7955	-	espL1	100.0	96.2	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00333	2661	3911	+	espR1	99.3	94.6	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00379	2299	3438	-	espR3	100.0	96.4	NP_288394	(espR3) Type III secretion system effector espR3 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00154	1505	3085	+	espX4	100.0	94.9	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00052	6106	8514	+	espY4	99.8	89.4	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00184	1435	5648	+	fdeC	99.1	92.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00023	4704	6944	-	fepA	100.0	98.0	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00551	345	1301	+	fepB	100.0	98.1	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	13833	14648	-	fepC	100.0	97.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	15634	16482	-	fepD	83.5	96.7	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	14645	15637	-	fepG	100.0	95.3	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	7187	8389	+	fes	100.0	99.3	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00958	275	1477	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00179	598	1131	+	fimF	100.0	97.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00179	1144	1647	+	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00179	1658	2569	+	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	5862	7883	+	fyuA	100.0	100.0	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	42667	43497	-	gspC	100.0	94.8	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	40577	42427	-	gspD	100.0	94.8	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	39084	40577	-	gspE	100.0	94.5	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	37885	39084	-	gspF	100.0	94.1	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	37389	37844	-	gspG	100.0	96.3	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	36822	37352	-	gspH	100.0	97.2	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	36454	36825	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	35852	36421	-	gspJ	100.0	96.3	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	34878	35855	-	gspK	100.0	97.2	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	33703	34563	-	gspL	100.0	95.0	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	33166	33587	-	gspM	99.8	95.7	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00031	6058	7845	+	iucA	100.0	94.3	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00031	7846	8793	+	iucB	100.0	95.7	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00031	8793	10535	+	iucC	100.0	96.1	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00031	10532	11853	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00031	11791	14092	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00001	19000	20676	+	kpsD	100.0	98.0	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00001	31328	32104	-	kpsM	100.0	92.7	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig01031	64	1116	-	ompA	100.0	95.5	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00796	957	1508	+	papX	100.0	97.5	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00072	1857	3839	-	shuA	100.0	98.3	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00072	6807	7301	+	shuX	100.0	96.2	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00252	3222	3975	-	yagV/ecpE	99.7	97.6	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00207	2928	5453	+	yagX/ecpC	100.0	98.5	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00207	2234	2902	+	yagY/ecpB	100.0	98.8	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00207	1589	2176	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00769	1	777	+	ybtA	80.9	100.0	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00002	4154	5731	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00750	1	1778	-	ybtP	98.6	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig01030	1	1498	+	ybtQ	83.1	100.0	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00756	815	2070	+	ybtS	96.2	97.5	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00002	3347	4150	+	ybtT	100.0	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00002	2250	3350	+	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00207	924	1514	+	ykgK/ecpR	100.0	99.7	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID014at24

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00066	9207	9512	-	afaA	100.0	100.0	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00066	8172	8916	-	afaB-I	100.0	99.6	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00066	5497	8079	-	afaC-I	100.0	99.9	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00066	5038	5481	-	afaD	100.0	100.0	CAW30800	(afaD) AfaD [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00066	3800	4285	-	afaE-I	100.0	99.8	CAW30801	(afaE-I) AFA-I adhesin [Afa/Dr family (VF0212)] [Escherichia coli O25b:H4 str. FV9863]
contig00161	2910	4338	+	aslA	100.0	92.9	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig01375	214	1602	+	aslA	97.2	98.1	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00114	6328	6651	+	cesAB	100.0	100.0	NP_290286	(cesAB) chaperone for EspA and EspB [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	18724	19179	+	cesD	100.0	99.8	NP_290276	(cesD) chaperone for EspB and EspD [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933]
contig00203	3210	3617	+	cesD2	100.0	99.0	NP_290253	(cesD2) chaperone for EspD [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	14838	15191	-	cesL	100.0	99.4	NP_290270	(cesL) chaperone for SepL [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	5261	5731	-	cesT	100.0	95.5	NP_290260	(cesT) multieffector chaperone [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00101	1448	3394	-	chuA	100.0	99.5	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00101	371	1399	-	chuS	100.0	99.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00101	4036	5028	+	chuT	100.0	99.8	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig01045	927	1727	-	chuV	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00101	5048	6385	+	chuW	100.0	98.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00101	6398	6892	+	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00101	6892	7515	+	chuY	100.0	98.2	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig03350	48	503	+	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig01868	638	1054	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00681	1	690	+	csgG	82.7	84.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig02263	298	987	-	csgG	82.7	83.6	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00066	4487	4660	-	draP	100.0	98.8	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00005	2672	5201	-	eae	89.3	90.5	AAC38392	(eae) intimin [Intimin (VF0177)] [Escherichia coli O127:H6 str. E2348/69]
contig00057	3541	4287	+	entA	100.0	96.4	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00057	2684	3541	+	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00057	1	1050	+	entC	88.4	97.0	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00745	153	1340	+	entC	100.0	98.7	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00156	310	971	+	entD	85.9	96.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01895	106	876	-	entD	100.0	94.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00057	1060	2670	+	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00037	3361	7214	+	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00957	963	2174	-	entS	96.9	96.0	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig01765	55	1266	-	entS	96.9	97.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00005	17172	18710	+	escC	100.0	99.6	NP_290275	(escC) Type III secretion system secretin EscC [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933]
contig00005	751	1971	+	escD	100.0	98.7	NP_290258	(escD) Type III secretion system outer MS ring protein EscD [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933]
contig00114	6106	6324	+	escE	100.0	98.6	NP_290287	(escE) chaperone for EscF [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00203	3653	3874	+	escF	100.0	100.0	NP_290252	(escF) Type III secretion system needle filament protein EscF [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933]
contig00203	3880	4158	+	escG	100.0	97.8	NP_290251	(escG) chaperone for EscF [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	15708	16136	+	escI	100.0	99.3	NP_290272	(escI) Type III secretion system inner rod component EscI [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	16139	16711	+	escJ	100.0	99.5	NP_290273	(escJ) Type III secretion system inner MS ring protein EscJ [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933]
contig00114	7273	7795	+	escL	85.0	99.4	NP_290284	(escL) negative regulator EscL stator protein [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	11490	12830	-	escN	100.0	99.5	NP_290268	(escN) ATPase EscN [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933]
contig00005	11110	11487	-	escO	100.0	99.7	NP_290267	(escO) positive regulator EscO [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	10701	10976	-	escP	100.0	99.3	NP_290266	(escP) Type III secretion system needle length regulator EscP [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	23129	23782	-	escR	100.0	99.8	NP_290283	(escR) Type III secretion systemminor export apparatus protein EscR [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933]
contig00005	22860	23129	-	escS	100.0	100.0	NP_290282	(escS) Type III secretion systemminor export apparatus protein EscS [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933]
contig00005	22084	22860	-	escT	100.0	99.6	NP_290281	(escT) Type III secretion system minor export apparatus protein EscT [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933]
contig00005	21054	22091	-	escU	100.0	99.6	NP_290280	(escU) Type III secretion system export apparatus switch protein EscU [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933]
contig00005	12814	14841	-	escV	100.0	99.8	NP_290269	(escV) Type III secretion system major export apparatus protein [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933]
contig00203	484	1062	+	espA	100.0	84.6	NP_290256	(espA) Type III secretion system translocator protein EspA [EspA (VF0198)] [Escherichia coli O157:H7 str. EDL933]
contig00203	2238	3203	+	espB	100.0	99.9	AAC38396	(espB) EspB [EspB (VF0179)] [Escherichia coli O127:H6 str. E2348/69]
contig00203	1075	2217	+	espD	100.0	99.7	AAC38395	(espD) EspD [EspD (VF0180)] [Escherichia coli O127:H6 str. E2348/69]
contig00203	4243	4863	+	espF	100.0	99.7	AAC38400	(espF) EspF [EspF (VF0182)] [Escherichia coli O127:H6 str. E2348/69]
contig00114	3255	4451	-	espG	100.0	98.5	NP_290289	(espG) Type III secretion system effector EspG GTPase activating protein [EspG (VF0201)] [Escherichia coli O157:H7 str. EDL933]
contig00071	606	1967	+	espK	100.0	92.1	NP_287316	(espK) Type III secretion system effector EspK [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00778	254	2152	+	espL1	100.0	96.4	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00071	2344	5157	-	espN	100.0	99.9	NP_287312	(espN) Type III secretion system effector EspN [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00388	1875	2929	+	espR1	83.7	94.0	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00252	2957	4537	+	espX4	99.9	94.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00295	1566	2858	-	espX5	100.0	96.5	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00071	6337	8286	-	espX7/nleL	100.0	99.7	NP_287310	(espX7/nleL) Type III secretion system effector NleL putative E3 ubiquitin ligase [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	20599	21057	+	etgA	100.0	99.1	NP_290279	(etgA) T3SS-associated peptidoglycan lytic enzyme [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00957	3	959	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00037	8588	9403	-	fepC	100.0	97.4	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00037	10389	11300	-	fepD	89.7	95.6	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01231	1	918	+	fepD	90.3	97.6	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00037	9400	10392	-	fepG	100.0	94.5	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01231	915	1767	+	fepG	85.9	98.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00037	1941	3143	+	fes	100.0	96.5	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00632	1561	2172	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig02935	1	538	+	fimA	88.8	89.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00632	195	920	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig02144	397	930	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig02871	146	679	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00312	109	1020	+	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00632	957	1496	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00022	9656	10486	-	gspC	100.0	96.5	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00022	7566	9416	-	gspD	100.0	97.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00022	6073	7566	-	gspE	100.0	96.5	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00452	142	1635	+	gspE	100.0	95.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00022	4874	6073	-	gspF	100.0	95.9	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00452	1635	2834	+	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00022	4378	4833	-	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00452	2875	3330	+	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00022	3811	4341	-	gspH	100.0	95.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00022	3443	3814	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00808	1961	2332	-	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00022	2841	3410	-	gspJ	100.0	96.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00808	1359	1928	-	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00022	1867	2844	-	gspK	100.0	97.8	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00808	385	1362	-	gspK	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00022	692	1552	-	gspL	100.0	97.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00022	154	576	-	gspM	100.0	97.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00421	2643	3064	-	gspM	99.8	92.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00025	5316	7097	-	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00025	4368	5315	-	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00025	2626	4368	-	iucC	100.0	98.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00025	1308	2629	-	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00079	3333	5009	+	kpsD	100.0	98.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00421	808	1584	-	kpsM	100.0	94.7	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00005	7835	8446	-	map	100.0	82.3	NP_290262	(map) Type III secretion system effector Map Rho guanine exchange factor [Map (VF0195)] [Escherichia coli O157:H7 str. EDL933]
contig00190	3576	4901	+	nleA/espI	100.0	89.5	NP_287961	(nleA/espI) Type III secretion system effector NleA [NleA/EspI (VF0338)] [Escherichia coli O157:H7 str. EDL933]
contig00363	3097	4077	-	nleB2	100.0	100.0	NP_286532	(nleB2) Type III secretion system effector NleB2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00363	920	1489	-	nleF	100.0	94.9	NP_287958	(nleF) Type III secretion system effector NleF caspase inhibitor [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00363	1544	2455	-	nleH2	99.9	91.6	NP_287959	(nleH2) Type III secretion system effector NleH2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig01215	745	1058	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig01215	1463	1696	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig01784	255	806	+	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00065	6246	7384	+	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00005	16717	17172	+	sepD	100.0	98.7	NP_290274	(sepD) Type III secretion system secretion switch protein SepD [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	9821	10738	-	sepQ/escQ	100.0	95.2	NP_290265	(sepQ/escQ) Type III secetion system C ring protein EscQ [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933]
contig00005	15376	15675	+	sepZ/espZ	100.0	99.7	NP_290271	(sepZ/espZ) Type III secretion system effector EspZ [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933]
contig00007	893	1646	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00496	1066	3401	+	yagX/ecpC	92.5	98.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00496	372	1040	+	yagY/ecpB	100.0	98.2	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig03163	54	661	+	yagY/ecpB	90.9	97.9	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01722	1	1287	+	ybtE	81.6	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00880	744	2024	-	ybtX	100.0	97.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00885	744	2024	-	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00150	6171	6761	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID015HW

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00061	7875	8619	-	afaB-I	100.0	98.2	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00061	5200	7782	-	afaC-I	100.0	99.0	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00025	49693	50148	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00025	50902	51552	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00025	51971	52387	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00025	52414	53247	+	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00061	9989	10216	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00061	8880	9185	-	draA	100.0	100.0	AAK16475	(draA) cytoplamic protein DraA [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00061	4741	5184	-	draD	100.0	99.8	AAK16478	(draD) DraD periplasmic protein [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00061	3443	4002	-	draE2	99.6	99.6	AAB65153	(draE2) Dr-II structural adhesin precursor [Afa/Dr family (VF0212)] [Escherichia coli EC7372]
contig00061	4189	4362	-	draP	100.0	99.4	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00012	99201	99947	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	99947	100804	-	entB	100.0	97.5	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	102438	103625	-	entC	100.0	97.4	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	118270	119040	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	100818	102428	-	entE	100.0	96.0	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	110513	114342	-	entF	98.7	95.9	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	104948	106198	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00017	5445	7343	-	espL1	100.0	94.8	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00051	24864	25919	+	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	116391	117812	+	espX1	100.0	94.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	62207	63787	-	espX4	99.9	92.9	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	31357	32649	+	espX5	100.0	95.6	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	28661	32886	+	fdeC	99.4	91.0	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00012	116005	118245	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	103988	104944	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	108299	109114	+	fepC	100.0	97.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	106297	107313	+	fepD	100.0	96.4	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	107310	108302	+	fepG	100.0	94.8	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	114560	115762	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00053	25212	25817	-	fimA	100.0	92.9	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00054	1111	1713	-	fimB	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	23846	24571	-	fimC	100.0	98.2	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	21143	23779	-	fimD	100.0	98.8	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00054	39	633	-	fimE	99.7	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	20603	21136	-	fimF	100.0	97.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	20087	20590	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	19165	20076	-	fimH	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	24608	25147	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00009	97658	98488	-	gspC	100.0	95.0	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	95568	97418	-	gspD	100.0	97.3	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	94075	95568	-	gspE	100.0	96.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	92876	94075	-	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	92380	92835	-	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	91813	92343	-	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	91445	91816	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	90843	91412	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	89869	90846	-	gspK	100.0	97.8	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	88694	89554	-	gspL	100.0	97.0	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	88156	88578	-	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	205158	206210	-	ompA	100.0	94.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00013	18802	19555	-	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	19479	21122	-	yagW/ecpD	100.0	98.6	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	21112	23637	-	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	23663	24331	-	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	24389	24976	-	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	25051	25641	-	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID015at48

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00071	5613	6357	-	afaB-I	100.0	98.2	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00071	2938	5520	-	afaC-I	100.0	99.0	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00006	132424	132879	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	133633	134283	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	134702	135118	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	135145	135978	+	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00071	7727	7954	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00071	6618	6923	-	draA	100.0	100.0	AAK16475	(draA) cytoplamic protein DraA [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00071	2479	2922	-	draD	100.0	99.8	AAK16478	(draD) DraD periplasmic protein [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00071	1181	1740	-	draE2	99.6	99.6	AAB65153	(draE2) Dr-II structural adhesin precursor [Afa/Dr family (VF0212)] [Escherichia coli EC7372]
contig00071	1927	2100	-	draP	100.0	99.4	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00040	23172	23918	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	23918	24775	-	entB	100.0	97.5	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	26409	27596	-	entC	100.0	97.4	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	42241	43011	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	24789	26399	-	entE	100.0	96.0	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	34484	38313	-	entF	98.7	95.9	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	28919	30169	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00033	26358	28256	+	espL1	100.0	94.8	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00042	14590	15645	-	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00025	50896	52317	+	espX1	100.0	94.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00010	62182	63762	-	espX4	99.9	92.9	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00010	31332	32624	+	espX5	100.0	95.6	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	83053	87278	-	fdeC	99.4	91.0	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00040	39976	42216	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	27959	28915	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	32270	33085	+	fepC	100.0	97.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	30268	31284	+	fepD	100.0	96.4	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	31281	32273	+	fepG	100.0	94.8	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	38531	39733	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00019	77242	77847	-	fimA	100.0	92.9	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00057	25726	26328	+	fimB	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	75876	76601	-	fimC	100.0	98.2	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	73173	75809	-	fimD	100.0	98.8	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00057	26806	27400	+	fimE	99.7	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	72633	73166	-	fimF	100.0	97.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	72117	72620	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	71195	72106	-	fimH	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	76638	77177	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00004	136126	136956	-	gspC	100.0	95.0	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	134036	135886	-	gspD	100.0	97.3	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	132543	134036	-	gspE	100.0	96.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	131344	132543	-	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	130848	131303	-	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	130281	130811	-	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	129913	130284	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	129311	129880	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	128337	129314	-	gspK	100.0	97.8	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	127162	128022	-	gspL	100.0	97.0	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	126624	127046	-	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	83583	84635	-	ompA	100.0	94.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00052	22274	23027	-	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00052	22951	24594	-	yagW/ecpD	100.0	98.6	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00052	24584	27109	-	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00052	27135	27803	-	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00052	27861	28448	-	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00052	28523	29113	-	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID016at24

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00033	254	1682	-	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00002	148976	149431	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00002	147569	148219	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00002	146734	147150	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00002	145874	146707	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00045	18008	18754	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00045	18754	19611	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00045	21245	22432	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00045	37076	37846	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00045	19625	21235	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00045	29295	33148	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00045	23755	25005	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00021	15786	17686	+	espL1	100.0	97.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00011	102778	104964	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00047	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	69187	70608	-	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00011	72982	74562	-	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00011	42191	43483	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	108754	109565	+	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00026	59008	63256	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00045	34811	37051	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00045	22795	23751	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00045	27106	27921	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00045	25104	26120	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00045	26117	27109	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00045	33366	34568	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00063	25238	25849	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00063	23872	24597	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00063	21169	23805	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00063	20629	21162	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00063	20113	20616	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00063	19191	20102	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00063	24634	25173	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00031	31681	33702	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	18581	28072	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	12386	18493	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00002	65175	66215	-	ompA	100.0	98.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00036	8091	8844	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00036	6524	8167	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00036	4009	6534	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00036	3315	3983	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00036	2670	3257	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	11236	12195	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	29973	31550	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	9267	11069	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	7478	9280	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	4873	6177	-	ybtS	100.0	99.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	29166	29969	+	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	28069	29169	+	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	6205	7485	-	ybtX	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	2005	2595	+	ykgK/ecpR	100.0	96.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID017at48

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00013	34713	36141	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00030	6293	6748	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00030	4886	5536	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00030	4051	4467	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00030	3191	4024	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00041	19920	20666	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00041	20666	21523	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00041	23157	24344	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00041	38988	39758	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00041	21537	23147	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00041	31207	35060	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00041	25667	26917	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00022	23929	25829	+	espL1	100.0	97.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00075	14097	16283	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00057	25069	26122	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015	50505	51926	-	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00055	13970	15550	+	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00024	40679	41971	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00045	17064	17875	-	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00010	33538	37786	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00041	36723	38963	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00041	24707	25663	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00041	29018	29833	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00041	27016	28032	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00041	28029	29021	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00041	35278	36480	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00069	25027	25638	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00069	23661	24386	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00069	20958	23594	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00069	20418	20951	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00069	19902	20405	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00069	18980	19891	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00069	24423	24962	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00025	30503	32524	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	17403	26894	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	11208	17315	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00007	14845	15885	-	ompA	100.0	98.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00010	46897	47650	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00010	45330	46973	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00010	42815	45340	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00010	42121	42789	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00010	41476	42063	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00025	10058	11017	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	28795	30372	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	8089	9891	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	6300	8102	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	3695	4999	-	ybtS	100.0	99.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	27988	28791	+	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	26891	27991	+	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	5027	6307	-	ybtX	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00010	40811	41401	+	ykgK/ecpR	100.0	96.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID018at24

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00016	74847	76275	+	aslA	100.0	98.5	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00005	177711	179657	-	chuA	100.0	99.7	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00005	176634	177662	-	chuS	100.0	99.5	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00005	180299	181291	+	chuT	100.0	99.7	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00005	183827	184819	+	chuU	100.0	99.5	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00005	184786	185586	+	chuV	100.0	99.6	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00005	181311	182648	+	chuW	100.0	99.1	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00005	182661	183155	+	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00005	183155	183778	+	chuY	100.0	98.4	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00011	80832	81287	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	82040	82690	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	83109	83525	+	csgF	99.0	80.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	83552	84385	+	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00037	31204	31950	-	entA	100.0	98.4	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00037	31950	32807	-	entB	100.0	99.2	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00037	34441	35628	-	entC	100.0	99.7	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00041	4966	5627	+	entD	85.9	92.8	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00037	32821	34431	-	entE	100.0	99.1	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00037	36765	38015	-	entS	100.0	98.8	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00050	22805	26613	-	fdeC	89.6	99.6	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00041	2701	4941	+	fepA	100.0	98.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00037	35805	36761	+	fepB	100.0	99.8	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00037	40116	40931	+	fepC	100.0	99.4	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00037	38114	39130	+	fepD	100.0	99.5	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00037	39127	40119	+	fepG	100.0	99.8	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00041	1256	2458	-	fes	100.0	99.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00013	126236	126841	-	fimA	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00033	1122	1724	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	124870	125595	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	122167	124803	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00033	48	644	-	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	121627	122160	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	121111	121614	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	120189	121100	-	fimH	100.0	97.2	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	125632	126171	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00018	86035	88056	-	fyuA	100.0	100.0	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	170339	171169	+	gspC	100.0	93.9	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	171409	173259	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	173259	174752	+	gspE	100.0	94.9	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	174752	175951	+	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	175992	176447	+	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	176484	177014	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	177011	177382	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	177415	177984	+	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	177981	178958	+	gspK	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	179273	180133	+	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	180249	180670	+	gspM	99.8	93.6	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00021	3195	12686	-	irp1	100.0	99.3	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	12776	18880	-	irp2	100.0	98.9	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00053	10165	11946	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00053	11947	12894	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00053	12894	14636	+	iucC	100.0	98.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00053	14633	15954	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00053	15892	18193	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00004	193824	195500	-	kpsD	100.0	99.0	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00004	181730	182506	+	kpsM	100.0	99.9	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00004	182503	183162	+	kpsT	100.0	100.0	AAA24047	(kpsT) KpsT [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00008	140930	141970	-	ompA	100.0	99.5	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00053	747	1060	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00053	1465	1698	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00098	256	807	+	papX	100.0	97.5	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00082	151	4051	+	sat	100.0	99.5	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00067	8438	9576	+	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00038	20107	24238	+	vat	100.0	99.7	NP_752330	(vat) Haemoglobin protease [Tsh (VF0233)] [Escherichia coli CFT073]
contig00038	15737	16490	+	yagV/ecpE	99.7	98.4	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00038	14170	15813	+	yagW/ecpD	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00038	11655	14180	+	yagX/ecpC	100.0	97.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00038	10961	11629	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00038	10317	10904	+	yagZ/ecpA	100.0	98.5	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00021	19071	20030	-	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	1	1294	-	ybtE	82.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	20197	21999	+	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	21986	23788	+	ybtQ	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	25089	26393	+	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	1298	2101	-	ybtT	100.0	99.5	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	2098	3198	-	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	23781	25061	+	ybtX	100.0	99.6	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00038	9652	10242	+	ykgK/ecpR	100.0	99.3	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID020at24

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00030	15483	16911	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00019	7466	7921	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00019	6061	6711	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00019	5226	5642	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00019	4366	5199	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	26547	27293	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00032	27293	28150	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00032	29784	30971	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00032	45615	46385	+	entD	100.0	95.1	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00032	28164	29774	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00032	37834	41687	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00032	32294	33544	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00009	15959	17858	-	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00012	91954	94140	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00060	15211	16264	-	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00002	190820	191954	-	espR4	99.5	84.3	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	144042	145463	+	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00012	62158	63738	-	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00012	31367	32659	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	105100	105896	-	espY1	99.9	88.7	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00040	4769	9017	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00032	43350	45590	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00032	31334	32290	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00032	35645	36460	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00032	33643	34659	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00032	34656	35648	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00032	41905	43107	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00014	53037	53648	-	fimA	100.0	88.4	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	55146	55748	-	fimB	100.0	98.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	51671	52396	-	fimC	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	48968	51604	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	54075	54669	-	fimE	99.7	99.3	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	48428	48961	-	fimF	100.0	97.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	47912	48415	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	46990	47901	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	52433	52972	-	fimI	100.0	98.9	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00007	134529	135359	-	gspC	100.0	94.7	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	132439	134289	-	gspD	100.0	96.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	130946	132439	-	gspE	100.0	96.9	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	129747	130946	-	gspF	100.0	96.0	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	129251	129706	-	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	128684	129214	-	gspH	100.0	95.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	128316	128687	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	127714	128283	-	gspJ	100.0	96.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	126740	127717	-	gspK	100.0	97.0	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	125565	126425	-	gspL	100.0	97.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	125027	125449	-	gspM	100.0	98.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	237168	238208	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00040	18126	18879	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00040	16559	18202	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00040	14044	16569	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00040	13350	14018	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00040	12705	13292	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00040	12040	12630	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID021at24

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00029	16207	17635	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00004	135844	136299	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00004	137054	137704	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00004	138123	138539	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00004	138566	139399	+	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00071	19198	19944	+	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00071	18341	19198	+	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00071	15520	16707	+	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00071	106	876	-	entD	100.0	94.3	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00071	16717	18327	+	entE	100.0	95.4	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00071	4804	8657	+	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00071	12947	14197	+	entS	100.0	95.5	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00014	1	1859	+	espL1	97.8	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00020	17395	18975	-	espX4	99.9	94.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00055	19768	21060	+	espX5	100.0	96.6	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00071	901	3141	-	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00071	14201	15157	-	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00071	10031	10846	-	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00071	11832	12848	-	fepD	100.0	96.2	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00071	10843	11835	-	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00071	3384	4586	+	fes	100.0	96.6	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00061	25661	28297	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00061	25121	25654	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00061	24605	25108	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00061	23683	24594	-	fimH	100.0	97.2	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00056	29400	31421	+	fyuA	100.0	99.6	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00056	16300	25791	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00056	10105	16212	+	irp2	100.0	99.6	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	29720	30772	+	ompA	100.0	95.6	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00097	3621	4559	-	pla	100.0	98.3	NP_395233	(pla) plasminogen activator protease precursor [Pla (VF0139)] [Yersinia pestis CO92]
contig00056	8955	9914	+	ybtA	100.0	99.3	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00056	27692	29269	+	ybtE	100.0	99.9	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00056	6986	8788	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00056	5197	6999	-	ybtQ	100.0	99.6	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00056	2592	3896	-	ybtS	100.0	99.5	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00056	26885	27688	+	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00056	25788	26888	+	ybtU	100.0	99.9	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00056	3924	5204	-	ybtX	100.0	99.6	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]

ID025III

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00816	681	1331	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig02160	275	691	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig01530	11	757	+	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00746	403	1499	-	entS	87.7	95.1	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00565	1	1436	+	espX4	90.8	93.7	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00071	1520	2245	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00201	1174	1707	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00201	658	1161	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00071	2282	2821	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00782	36	1340	-	ybtS	100.0	99.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00091	411	1214	-	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00091	1211	2311	-	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]

ID025II

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00018	49173	50601	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00038	6313	6768	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00038	4906	5556	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00038	4071	4487	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00038	3211	4044	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00049	18008	18754	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00049	18754	19611	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00049	21245	22432	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00049	37076	37846	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00049	19625	21235	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00049	29295	33148	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00049	23755	25005	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00037	1	1621	+	espL1	85.3	97.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00025	63986	66172	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00052	24678	25731	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00035	46284	47705	+	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00025	34190	35770	-	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00025	3399	4691	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00035	7327	8138	-	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00022	33602	37850	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00049	34811	37051	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00049	22795	23751	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00049	27106	27921	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00049	25104	26120	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00049	26117	27109	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00049	33366	34568	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00061	25238	25849	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00061	23872	24597	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00061	21169	23805	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00061	20629	21162	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00061	20113	20616	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00061	19191	20102	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00061	24634	25173	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00036	30503	32524	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	17403	26894	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	11208	17315	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00002	103766	104806	-	ompA	100.0	98.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00022	46961	47714	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	45394	47037	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	42879	45404	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	42185	42853	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	41540	42127	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00036	10058	11017	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	28795	30372	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	8089	9891	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	6300	8102	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	3695	4999	-	ybtS	100.0	99.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	27988	28791	+	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	26891	27991	+	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	5027	6307	-	ybtX	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00022	40875	41465	+	ykgK/ecpR	100.0	96.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID025I

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00026	24374	25802	-	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00001	301680	302135	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	300273	300923	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	299438	299854	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	298578	299411	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00052	8404	9150	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	9150	10007	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	11641	12828	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	27472	28242	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	10021	11631	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	19691	23544	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	14151	15401	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00024	23931	25831	+	espL1	100.0	97.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	102815	105001	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00042	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	50505	51926	-	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	73019	74599	-	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	42228	43520	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	90072	90883	+	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00014	58848	63096	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00052	25207	27447	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	13191	14147	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	17502	18317	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	15500	16516	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	16513	17505	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	23762	24964	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00053	25238	25849	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	23872	24597	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	21169	23805	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	20629	21162	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	20113	20616	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	19191	20102	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	24634	25173	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	30503	32524	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00035	17403	26894	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00035	11208	17315	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	217879	218919	-	ompA	100.0	98.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00014	72207	72960	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00014	70640	72283	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00014	68125	70650	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00014	67431	68099	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00014	66786	67373	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00035	10058	11017	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00035	28795	30372	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00035	8089	9891	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00035	6300	8102	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00035	3695	4999	-	ybtS	100.0	99.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00035	27988	28791	+	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00035	26891	27991	+	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00035	5027	6307	-	ybtX	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00014	66121	66711	+	ykgK/ecpR	100.0	96.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID026

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00021	49173	50601	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00035	9327	9782	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00035	7920	8570	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00035	7085	7501	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00035	6225	7058	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00044	18008	18754	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	18754	19611	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	21245	22432	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	37076	37846	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	19625	21235	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	29295	33148	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	23755	25005	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00024	23931	25831	+	espL1	100.0	97.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	91986	94172	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00045	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	69187	70608	-	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	62190	63770	-	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	31399	32691	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	108754	109565	+	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00002	204827	209075	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00044	34811	37051	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	22795	23751	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	27106	27921	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	25104	26120	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	26117	27109	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	33366	34568	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00055	25238	25849	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00055	23872	24597	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00055	21169	23805	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00055	20629	21162	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00055	20113	20616	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00055	19191	20102	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00055	24634	25173	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00033	30503	32524	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	17403	26894	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	11208	17315	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	219469	220509	-	ompA	100.0	98.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00002	218186	218939	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	216619	218262	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	214104	216629	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	213410	214078	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	212765	213352	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00033	10058	11017	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	28795	30372	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	8089	9891	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	6300	8102	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	3695	4999	-	ybtS	100.0	99.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	27988	28791	+	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	26891	27991	+	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	5027	6307	-	ybtX	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00002	212100	212690	+	ykgK/ecpR	100.0	96.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID027

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00023	49173	50601	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00035	6471	6926	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00035	5064	5714	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00035	4229	4645	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00035	3369	4202	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00044	18008	18754	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	18754	19611	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	21245	22432	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	37076	37846	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	19625	21235	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	29295	33148	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	23755	25005	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00026	23930	25830	+	espL1	100.0	97.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	7562	9748	-	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00045	25726	26779	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00012	69187	70608	-	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	37964	39544	+	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	69043	70335	-	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00012	108754	109565	+	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00025	33539	37787	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00044	34811	37051	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	22795	23751	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	27106	27921	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	25104	26120	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	26117	27109	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	33366	34568	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00058	25238	25849	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00058	23872	24597	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00058	21169	23805	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00058	20629	21162	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00058	20113	20616	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00058	19191	20102	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00058	24634	25173	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00054	20731	22752	-	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00060	11208	17315	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	177939	178979	-	ompA	100.0	98.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00025	46898	47651	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00025	45331	46974	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00025	42816	45341	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00025	42122	42790	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00025	41477	42064	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00060	10058	11017	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00054	22883	24460	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00060	8089	9891	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00060	6300	8102	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00060	3695	4999	-	ybtS	100.0	99.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00054	24464	25267	-	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00054	25264	26364	-	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00060	5027	6307	-	ybtX	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	40812	41402	+	ykgK/ecpR	100.0	96.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID031

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00018	75528	76955	+	aslA	99.9	98.0	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00009	179716	181662	-	chuA	100.0	99.8	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00009	178639	179667	-	chuS	100.0	99.5	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00009	182330	183322	+	chuT	100.0	99.5	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00009	185858	186850	+	chuU	100.0	99.6	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00009	186817	187617	+	chuV	100.0	99.6	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00009	183342	184679	+	chuW	100.0	99.1	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00009	184692	185186	+	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00009	185186	185809	+	chuY	100.0	99.5	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00042	7651	10695	+	cnf1	100.0	99.6	CAA50007	(cnf1) cytotoxic necrotizing factor 1 [CNF-1 (VF0240)] [Escherichia coli str. E-B35]
contig00021	88421	88876	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00021	89630	90280	+	csgD	100.0	81.4	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00021	90699	91115	+	csgF	99.0	81.7	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00021	91142	91975	+	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	97918	98664	-	entA	100.0	98.5	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	98664	99521	-	entB	100.0	99.3	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	101155	102342	-	entC	100.0	99.8	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	116808	117578	+	entD	100.0	97.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	99535	101145	-	entE	100.0	99.2	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	109019	112872	-	entF	99.3	98.2	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	103479	104729	-	entS	100.0	96.3	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00004	151801	156051	+	fdeC	100.0	99.9	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00016	114534	116783	+	fepA	100.0	98.1	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	102519	103475	+	fepB	100.0	99.6	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	106830	107645	+	fepC	100.0	100.0	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	104828	105844	+	fepD	100.0	98.5	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	105841	106833	+	fepG	100.0	99.2	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	113090	114292	-	fes	100.0	99.2	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00002	14738	15343	+	fimA	100.0	97.5	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	12638	13240	+	fimB	100.0	100.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	15984	16709	+	fimC	100.0	99.2	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	16775	19411	+	fimD	100.0	99.0	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	13718	14314	+	fimE	100.0	99.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	19418	19951	+	fimF	100.0	99.1	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	19964	20467	+	fimG	100.0	98.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	20478	21389	+	fimH	100.0	99.6	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	15408	15947	+	fimI	100.0	99.4	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00028	45687	46382	-	focC	100.0	99.6	NP_753155	(focC) F1C periplasmic chaperone [F1C fimbriae (VF0224)] [Escherichia coli CFT073]
contig00028	42987	45665	-	focD	100.0	99.8	NP_753156	(focD) F1C fimbrial usher [F1C fimbriae (VF0224)] [Escherichia coli CFT073]
contig00028	41922	42425	-	focG	100.0	100.0	NP_753158	(focG) F1C minor fimbrial subunit protein G presursor [F1C fimbriae (VF0224)] [Escherichia coli CFT073]
contig00028	40961	41971	-	focH	100.0	99.0	NP_753159	(focH) F1C Putative fimbrial adhesin precursor [F1C fimbriae (VF0224)] [Escherichia coli CFT073]
contig00011	29434	31455	-	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	122250	123080	-	gspC	100.0	94.0	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	120160	122010	-	gspD	100.0	94.4	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	118667	120160	-	gspE	100.0	93.4	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	117468	118667	-	gspF	100.0	93.6	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	116972	117427	-	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	116405	116935	-	gspH	100.0	92.8	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	116037	116408	-	gspI	100.0	93.3	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	115435	116004	-	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	114461	115438	-	gspK	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	113286	114146	-	gspL	100.0	94.9	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	112749	113170	-	gspM	99.8	93.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00042	1	3054	+	hlyA	99.3	99.2	NP_755445	(hlyA) Hemolysin A [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00042	3125	5248	+	hlyB	100.0	99.5	NP_755448	(hlyB) Hemolysin B [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00025	72150	72823	+	hlyC	99.8	99.0	NP_755444	(hlyC) Hemolysin C [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00042	5267	6703	+	hlyD	100.0	98.3	NP_755449	(hlyD) Hemolysin D [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00002	44055	45425	+	ibeA	99.9	98.6	AAF98391	(ibeA) invasion protein IbeA [Ibes (VF0237)] [Escherichia coli O18:K1:H7 str. RS218]
contig00041	1787	2949	+	iroB	99.9	98.4	NP_753168	(iroB) glucosyltransferase IroB [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00041	3012	6749	+	iroC	100.0	99.2	NP_753167	(iroC) ATP binding cassette transporter [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00041	6853	8082	+	iroD	100.0	98.9	NP_753166	(iroD) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00041	8167	9123	+	iroE	100.0	99.5	NP_753165	(iroE) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00041	9168	11345	-	iroN	100.0	99.1	NP_753164	(iroN) salmochelin receptor IroN [IroN (VF0230)] [Escherichia coli CFT073]
contig00011	35064	44555	-	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	44643	50750	-	irp2	100.0	98.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	97919	99595	+	kpsD	100.0	99.5	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00003	110913	111689	-	kpsM	100.0	99.9	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00003	110257	110916	-	kpsT	100.0	100.0	AAA24047	(kpsT) KpsT [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00006	175322	176362	-	ompA	100.0	99.5	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00003	10572	14081	-	pic	85.2	95.6	YP_006098864	(pic) Pic serine protease precursor autotransporter [Pic (VF0218)] [Escherichia coli O44:H18 042]
contig00028	47956	48285	-	sfaB	100.0	99.4	YP_540123	(sfaB) S fimbrial switch regulatory protein SfaB [S fimbriae (VF0222)] [Escherichia coli UTI89]
contig00028	48641	48925	+	sfaC	100.0	96.8	YP_540122	(sfaC) S fimbrial switch regulatory protein SfaC [S fimbriae (VF0222)] [Escherichia coli UTI89]
contig00028	46423	46971	-	sfaD	100.0	98.9	YP_540125	(sfaD) S fimbriae minor subunit SfaD [S fimbriae (VF0222)] [Escherichia coli UTI89]
contig00028	42447	42974	-	sfaG	100.0	100.0	YP_540128	(sfaG) S fimbriae minor subunit SfaG [S fimbriae (VF0222)] [Escherichia coli UTI89]
contig00028	39219	39770	-	sfaX	100.0	98.2	YP_540132	(sfaX) regulatory protein SfaX [S fimbriae (VF0222)] [Escherichia coli UTI89]
contig00028	39917	40657	-	sfaY	100.0	98.5	YP_540131	(sfaY) regulatory protein SfaY [S fimbriae (VF0222)] [Escherichia coli UTI89]
contig00011	74193	75116	-	tcpC	100.0	100.0	NP_754290	(tcpC) Tir domain containing protein TcpC [TcpC (VF0413)] [Escherichia coli CFT073]
contig00004	127965	132095	-	vat	100.0	100.0	NP_752330	(vat) Haemoglobin protease [Tsh (VF0233)] [Escherichia coli CFT073]
contig00004	135712	136465	-	yagV/ecpE	99.7	98.4	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00004	136389	138032	-	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00004	138022	140547	-	yagX/ecpC	100.0	97.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00004	140573	141241	-	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00004	141298	141885	-	yagZ/ecpA	100.0	98.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00011	50941	51900	-	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	31586	33163	-	ybtE	100.0	99.9	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	52067	53869	+	ybtP	100.0	99.8	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	53856	55658	+	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	56959	58263	+	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	33167	33970	-	ybtT	100.0	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	33967	35067	-	ybtU	100.0	99.9	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	55651	56931	+	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	141959	142549	-	ykgK/ecpR	100.0	99.3	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID032I

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00032	55910	56215	-	afaA	100.0	100.0	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00032	54868	55612	-	afaB-I	100.0	99.6	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00032	52193	54775	-	afaC-I	100.0	99.9	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00032	51734	52177	-	afaD	100.0	100.0	CAW30800	(afaD) AfaD [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00032	50496	50981	-	afaE-I	100.0	99.8	CAW30801	(afaE-I) AFA-I adhesin [Afa/Dr family (VF0212)] [Escherichia coli O25b:H4 str. FV9863]
contig00022	71077	72505	+	aslA	100.0	98.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00008	172126	174072	-	chuA	100.0	99.5	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	171049	172077	-	chuS	100.0	99.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	174714	175706	+	chuT	100.0	99.8	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	178242	179234	+	chuU	100.0	99.5	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	179201	180001	+	chuV	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	175726	177063	+	chuW	100.0	98.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	177076	177570	+	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	177570	178193	+	chuY	100.0	98.2	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00011	103007	103462	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	104215	104865	+	csgD	100.0	81.6	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	105284	105700	+	csgF	99.0	80.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	105727	106560	+	csgG	100.0	83.2	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	57133	57360	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00032	51183	51356	-	draP	100.0	98.8	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00006	150253	150999	-	entA	100.0	98.1	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	150999	151856	-	entB	100.0	99.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	153490	154677	-	entC	100.0	98.7	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	169166	169827	+	entD	85.9	96.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	151870	153480	-	entE	100.0	98.9	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	161357	165238	-	entF	100.0	98.2	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	155814	157064	-	entS	100.0	97.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	228836	233083	-	fdeC	99.9	97.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00006	166901	169141	+	fepA	100.0	98.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	154854	155810	+	fepB	100.0	98.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	159165	159980	+	fepC	100.0	99.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	157163	158179	+	fepD	100.0	97.8	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	158176	159168	+	fepG	100.0	97.9	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	165456	166658	-	fes	100.0	99.0	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00031	63484	64088	-	fimA	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00031	62118	62843	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00031	59415	62051	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00054	8989	9585	+	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00031	58875	59408	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00031	58359	58862	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00031	57437	58348	-	fimH	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00031	62880	63419	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00024	51772	53793	-	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00007	167409	168239	+	gspC	100.0	93.9	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	168479	170329	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	170329	171822	+	gspE	100.0	95.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	171822	173021	+	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	173062	173517	+	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	173554	174084	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	174081	174452	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	174485	175054	+	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	175051	176028	+	gspK	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	176343	177203	+	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	177319	177740	+	gspM	99.8	92.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00024	57402	66893	-	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	66981	73088	-	irp2	100.0	99.4	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00039	9495	11276	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00039	11277	12224	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00039	12224	13966	+	iucC	100.0	98.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00039	13963	15284	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00039	15222	17523	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00007	192461	194137	-	kpsD	100.0	98.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00007	178799	179575	+	kpsM	100.0	94.7	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00035	37571	38623	-	ompA	100.0	95.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00039	1409	1722	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00039	2127	2360	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00080	256	807	+	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00039	18455	22354	+	sat	100.0	99.6	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00001	248421	249174	+	yagV/ecpE	99.7	98.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	246854	248497	+	yagW/ecpD	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	244339	246864	+	yagX/ecpC	100.0	97.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	243645	244313	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	243001	243588	+	yagZ/ecpA	100.0	98.5	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00024	73279	74238	-	ybtA	100.0	99.3	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	53924	55501	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	74405	76207	+	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	76194	77996	+	ybtQ	100.0	99.6	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	79297	80601	+	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	55505	56308	-	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	56305	57405	-	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	77989	79269	+	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	242336	242926	+	ykgK/ecpR	100.0	99.5	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID033I

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00032	16542	17970	+	aslA	100.0	92.9	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00049	35888	36343	-	csgB	99.8	83.4	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	127197	127847	-	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	126362	126778	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	125502	126335	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00038	27334	28080	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	28080	28937	-	entB	100.0	98.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	30571	31758	-	entC	100.0	98.3	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	46402	47172	+	entD	100.0	95.1	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	28951	30561	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	38621	42474	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	33081	34331	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	78504	80404	-	espL1	100.0	97.4	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00046	14116	15170	-	espR1	83.7	93.9	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00022	64048	65468	+	espX1	99.9	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00010	37035	38615	+	espX4	99.9	94.0	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00010	68120	69412	-	espX5	100.0	97.0	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00022	24999	25780	-	espY1	99.9	90.4	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00081	2689	6937	+	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00038	44137	46377	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	32121	33077	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	36432	37247	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	34430	35446	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	35443	36435	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	42692	43894	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00051	2396	3007	-	fimA	100.0	88.1	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00051	4504	5106	-	fimB	100.0	97.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00051	1030	1755	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00051	3430	4026	-	fimE	100.0	99.5	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00056	28791	29324	-	fimF	100.0	99.1	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00056	28275	28778	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00056	27353	28264	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00051	1792	2331	-	fimI	100.0	99.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00006	54589	55629	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00035	6157	6910	+	yagV/ecpE	99.7	97.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00035	4590	6233	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00035	2076	4600	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00035	1382	2050	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00035	737	1324	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00035	72	662	+	ykgK/ecpR	100.0	96.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID034II

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00022	49173	50601	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00034	8088	8543	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00034	6681	7331	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00034	5846	6262	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00034	4986	5819	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00040	18008	18754	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	18754	19611	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	21245	22432	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	37076	37846	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	19625	21235	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	29295	33148	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	23755	25005	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00027	14871	16771	+	espL1	100.0	97.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	7232	9418	-	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00041	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	58678	60099	-	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	37634	39214	+	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	68713	70005	-	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	98245	99056	+	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00025	33554	37802	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00040	34811	37051	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	22795	23751	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	27106	27921	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	25104	26120	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	26117	27109	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00040	33366	34568	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00051	25238	25849	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00051	23872	24597	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00051	21169	23805	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00051	20629	21162	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00051	20113	20616	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00051	19191	20102	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00051	24634	25173	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00033	30503	32524	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	17403	26894	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	11208	17315	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	103766	104806	-	ompA	100.0	98.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00025	46912	47665	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00025	45345	46988	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00025	42830	45355	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00025	42136	42804	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00025	41491	42078	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00033	10058	11017	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	28795	30372	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	8089	9891	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	6300	8102	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	3695	4999	-	ybtS	100.0	99.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	27988	28791	+	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	26891	27991	+	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	5027	6307	-	ybtX	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	40826	41416	+	ykgK/ecpR	100.0	96.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID034I

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00020	49173	50601	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00033	8088	8543	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00033	6681	7331	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00033	5846	6262	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00033	4986	5819	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00044	18008	18754	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	18754	19611	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	21245	22432	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	37076	37846	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	19625	21235	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	29295	33148	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	23755	25005	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00023	23930	25830	+	espL1	100.0	97.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00026	57649	59835	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00046	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00002	50505	51926	-	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00026	27853	29433	-	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00037	1604	2896	-	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00002	90072	90883	+	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	204873	209121	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00044	34811	37051	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	22795	23751	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	27106	27921	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	25104	26120	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	26117	27109	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00044	33366	34568	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00053	25238	25849	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	23872	24597	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	21169	23805	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	20629	21162	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	20113	20616	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	19191	20102	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	24634	25173	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	30503	32524	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00038	17403	26894	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00038	11208	17315	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00005	103766	104806	-	ompA	100.0	98.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00001	218232	218985	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	216665	218308	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	214150	216675	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	213456	214124	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	212811	213398	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00038	10058	11017	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00038	28795	30372	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00038	8089	9891	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00038	6300	8102	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00038	3695	4999	-	ybtS	100.0	99.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00038	27988	28791	+	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00038	26891	27991	+	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00038	5027	6307	-	ybtX	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	212146	212736	+	ykgK/ecpR	100.0	96.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID037

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00111	327	1159	+	csgG	99.9	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00014	58920	59666	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	59666	60523	-	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	62157	63344	-	entC	100.0	97.6	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	77802	78572	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	60537	62147	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	70021	73874	-	entF	99.3	95.5	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	64481	65731	-	entS	100.0	95.7	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00062	10888	12787	+	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00097	8110	9165	+	espR1	83.8	94.3	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00021	62447	63790	+	espX1	94.5	95.3	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00014	75537	77777	+	fepA	100.0	97.2	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	63521	64477	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	67832	68647	+	fepC	100.0	96.6	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	65830	66846	+	fepD	100.0	95.5	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	66843	67835	+	fepG	100.0	94.8	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	74092	75294	-	fes	100.0	96.6	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00071	20418	20951	-	fimF	100.0	97.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00071	19902	20405	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00071	18980	19891	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00030	419	1249	+	gspC	100.0	95.2	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	1489	3339	+	gspD	100.0	97.8	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	3339	4832	+	gspE	100.0	96.8	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	4832	6031	+	gspF	100.0	95.9	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	6072	6527	+	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	6564	7094	+	gspH	100.0	94.9	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	7091	7462	+	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	7495	8064	+	gspJ	100.0	96.8	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	8061	9038	+	gspK	100.0	96.0	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	9353	10213	+	gspL	100.0	97.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	10329	10751	+	gspM	100.0	98.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	103916	104956	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]

ID043I

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00021	5141	5446	+	afaA	100.0	100.0	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00021	5744	6488	+	afaB-I	100.0	99.7	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00021	6581	9163	+	afaC-I	100.0	99.8	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00021	10369	10851	+	afaE-V	100.0	83.8	CAA62863	(afaE-V) AfaE-V adhesin [Afimbrial adhesin AFA-V (AI013)] [Escherichia coli str. AL 851]
contig00019	52979	54407	+	aslA	100.0	97.1	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00028	36589	37617	-	chuS	100.0	96.4	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00028	43781	44773	+	chuU	100.0	96.6	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00028	44740	45540	+	chuV	100.0	98.2	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00028	41265	42602	+	chuW	100.0	96.8	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00028	43109	43732	+	chuY	100.0	96.5	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00016	13752	14207	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	14962	15612	+	csgD	100.0	81.4	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	16031	16447	+	csgF	99.0	81.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	16474	17307	+	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00021	3996	4223	-	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00021	9179	9622	+	draD	100.0	99.8	AAK16478	(draD) DraD periplasmic protein [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00021	9994	10167	+	draP	100.0	98.8	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00011	87837	88583	-	entA	100.0	97.3	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	88583	89440	-	entB	100.0	98.8	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	91074	92261	-	entC	100.0	97.3	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	106719	107489	+	entD	100.0	92.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	89454	91064	-	entE	100.0	96.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	98938	102791	-	entF	99.3	95.5	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	93398	94648	-	entS	100.0	95.7	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	112360	114258	-	espL1	100.0	96.4	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00037	38824	41010	+	espL4	100.0	97.4	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00050	8773	10025	+	espR1	99.4	94.3	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	104206	105341	-	espR4	99.6	84.5	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	201678	203099	+	espX1	100.0	96.0	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00037	4962	6542	-	espX4	100.0	95.9	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	36414	37706	-	espX5	100.0	95.9	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	162243	162991	-	espY1	99.5	95.8	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	145208	145777	-	espY2	100.0	94.6	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00044	31222	32793	+	espY3	100.0	95.4	NP_286160	(espY3) Type III secretion system effector EspY3 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015	39565	41973	+	espY4	100.0	96.4	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	106400	110650	-	fdeC	100.0	95.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00011	104454	106694	+	fepA	100.0	96.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	92438	93394	+	fepB	100.0	97.7	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	96749	97564	+	fepC	100.0	96.9	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	94747	95763	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	95760	96752	+	fepG	100.0	94.2	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	103009	104211	-	fes	100.0	96.6	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00035	21384	21989	-	fimA	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	23487	24089	-	fimB	100.0	99.5	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	20018	20743	-	fimC	100.0	99.2	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	17316	19952	-	fimD	100.0	99.0	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	22413	23009	-	fimE	100.0	99.5	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	16776	17309	-	fimF	100.0	99.1	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	16260	16763	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	15338	16249	-	fimH	100.0	98.9	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	20780	21319	-	fimI	100.0	99.4	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00031	33458	35479	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00002	217159	217989	+	gspC	100.0	95.2	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	218229	220079	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	220079	221572	+	gspE	100.0	95.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	221572	222771	+	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	222812	223267	+	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	223304	223834	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	223831	224202	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	224235	224804	+	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	224801	225778	+	gspK	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	226093	226953	+	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	227069	227490	+	gspM	99.8	92.7	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00031	20358	29849	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	14163	20270	+	irp2	100.0	99.7	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00002	242211	243887	-	kpsD	100.0	98.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00002	228549	229325	+	kpsM	100.0	94.8	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00016	85780	86832	+	ompA	100.0	95.2	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00006	157140	157691	+	papX	100.0	97.5	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00028	37666	39648	-	shuA	100.0	98.5	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00028	40253	41245	+	shuT	100.0	98.1	YP_405017	(shuT) periplasmic binding protein ShuT [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00028	42615	43109	+	shuX	100.0	96.4	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00007	125982	126735	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00007	124415	126058	+	yagW/ecpD	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00007	121900	124425	+	yagX/ecpC	100.0	98.0	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00007	121206	121874	+	yagY/ecpB	100.0	98.4	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00007	120562	121149	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	13013	13972	+	ybtA	100.0	99.2	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	31750	33327	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	11044	12846	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	9255	11057	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	6650	7954	-	ybtS	100.0	99.7	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	30943	31746	+	ybtT	100.0	99.5	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	29846	30946	+	ybtU	100.0	99.1	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	7982	9262	-	ybtX	100.0	99.4	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00007	119897	120487	+	ykgK/ecpR	100.0	99.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID045

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00058	8036	8152	+	astA	100.0	99.1	BAA94855	(astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig00014	136791	137246	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00014	138000	138650	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00014	139069	139485	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00014	139512	140345	+	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00058	12954	13730	+	eltA	100.0	99.5	AAA24685	(eltA) heat-labile enterotoxin A prepeptide (from human) [Heat-labile toxin (LT) (VF0210)] [Escherichia coli]
contig00058	13727	14101	+	eltB	100.0	99.2	AAA98064	(eltB) enterotoxin subunit B (from human) [Heat-labile toxin (LT) (VF0210)] [Escherichia coli]
contig00015	99312	100058	-	entA	100.0	95.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	100058	100915	-	entB	100.0	97.8	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	102549	103736	-	entC	100.0	97.6	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	118381	119151	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	100929	102539	-	entE	100.0	96.0	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	110624	114453	-	entF	98.7	95.9	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	105059	106309	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00019	56923	58791	+	espL1	98.4	95.2	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	11959	13014	-	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00010	39315	40735	+	espX1	99.9	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	242755	244335	-	espX4	99.9	92.9	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	211962	213254	+	espX5	100.0	95.6	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00021	27502	31727	-	fdeC	99.4	91.1	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00015	116116	118356	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	104099	105055	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	108410	109225	+	fepC	100.0	97.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	106408	107424	+	fepD	100.0	95.6	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	107421	108413	+	fepG	100.0	94.7	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	114671	115873	-	fes	100.0	96.5	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00010	156459	157063	-	fimA	99.8	90.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00066	1111	1713	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	155093	155818	-	fimC	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	152390	155026	-	fimD	100.0	98.7	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00066	37	633	-	fimE	100.0	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	151850	152383	-	fimF	100.0	97.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	151334	151837	-	fimG	100.0	98.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	150412	151323	-	fimH	100.0	97.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	155855	156394	-	fimI	100.0	99.1	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	29070	29900	-	gspC	100.0	94.6	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00013	26980	28830	-	gspD	100.0	97.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00013	25487	26980	-	gspE	100.0	96.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00013	24288	25487	-	gspF	100.0	96.3	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00013	23792	24247	-	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00013	23225	23755	-	gspH	100.0	95.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00013	22857	23228	-	gspI	100.0	94.6	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00013	22255	22824	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00013	21281	22258	-	gspK	100.0	97.3	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00013	20106	20966	-	gspL	100.0	97.3	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00013	19568	19990	-	gspM	100.0	97.2	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	139311	140351	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00021	40833	41586	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00021	39266	40909	+	yagW/ecpD	100.0	98.6	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00021	36751	39276	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00021	36057	36725	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00021	35412	35999	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00021	34747	35337	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID047

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00019	53204	54632	+	aslA	100.0	96.9	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00012	74057	75085	+	chuS	100.0	97.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00012	66900	67892	-	chuU	100.0	98.8	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00012	66133	66933	-	chuV	100.0	98.2	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00012	69071	70408	-	chuW	100.0	97.0	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00012	67941	68564	-	chuY	100.0	96.6	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00021	49597	50052	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00021	50796	51446	+	csgD	100.0	81.4	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00021	51865	52281	+	csgF	99.0	81.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00021	52308	53141	+	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	65922	66668	-	entA	100.0	96.1	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	66668	67525	-	entB	100.0	98.5	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	69159	70346	-	entC	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	84804	85574	+	entD	100.0	92.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	67539	69149	-	entE	100.0	96.0	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	77023	80876	-	entF	99.3	95.5	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	71483	72733	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00002	226033	227931	-	espL1	100.0	96.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00061	6908	9094	+	espL4	100.0	96.5	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00034	45165	46586	+	espX1	100.0	94.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00011	25482	27062	+	espX4	100.0	96.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00011	56552	57844	-	espX5	100.0	96.3	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00034	5345	6093	-	espY1	99.5	95.6	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	145005	145574	-	espY2	100.0	94.7	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00025	8357	9928	-	espY3	100.0	95.7	NP_286160	(espY3) Type III secretion system effector EspY3 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	70981	73389	-	espY4	100.0	95.9	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	96395	100645	-	fdeC	100.0	95.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00006	82539	84779	+	fepA	100.0	96.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	70523	71479	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	74834	75649	+	fepC	100.0	96.7	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	72832	73848	+	fepD	100.0	95.9	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	73845	74837	+	fepG	100.0	93.8	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	81094	82296	-	fes	100.0	96.4	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00023	46260	46865	-	fimA	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00023	48363	48965	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00023	44894	45619	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00023	42191	44827	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00023	47289	47885	-	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00023	41651	42184	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00023	41135	41638	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00023	40213	41124	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00023	45656	46195	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00026	35971	37992	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00008	17255	18085	-	gspC	100.0	95.3	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	15165	17015	-	gspD	100.0	96.3	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	13672	15165	-	gspE	100.0	94.8	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	12473	13672	-	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	11977	12432	-	gspG	100.0	96.3	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	11410	11940	-	gspH	100.0	96.4	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	11042	11413	-	gspI	100.0	94.4	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	10440	11009	-	gspJ	100.0	96.0	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	9466	10443	-	gspK	100.0	96.9	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	8291	9151	-	gspL	100.0	93.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	7754	8175	-	gspM	99.8	94.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00026	22871	32362	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	16676	22783	+	irp2	100.0	99.7	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00062	2017	3798	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00062	3799	4746	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00062	4746	6488	+	iucC	100.0	98.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00062	6485	7806	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00062	7744	10045	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00059	11086	12762	-	kpsD	100.0	99.5	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00008	5920	6696	-	kpsM	100.0	94.8	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00010	102451	103503	-	ompA	100.0	95.2	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00083	749	1062	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00083	1467	1700	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00121	366	917	+	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00062	10977	14876	+	sat	100.0	99.6	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00072	8392	9530	+	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00012	72026	74008	+	shuA	100.0	98.7	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00012	70428	71420	-	shuT	100.0	97.9	YP_405017	(shuT) periplasmic binding protein ShuT [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00012	68564	69058	-	shuX	100.0	96.0	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00030	9764	10517	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00030	8197	9840	+	yagW/ecpD	100.0	98.8	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00030	5682	8207	+	yagX/ecpC	100.0	98.1	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00030	4988	5656	+	yagY/ecpB	100.0	97.9	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00030	4343	4930	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00026	15526	16485	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	34263	35840	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	13557	15359	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	11768	13570	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	9163	10467	-	ybtS	100.0	99.7	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	33456	34259	+	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	32359	33459	+	ybtU	100.0	99.9	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	10495	11775	-	ybtX	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00030	3678	4268	+	ykgK/ecpR	100.0	99.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID050

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00020	49279	50707	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00032	40481	40936	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	41691	42341	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	42760	43176	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	43203	44036	+	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00013	99075	99821	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	99821	100678	-	entB	100.0	98.0	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	102312	103499	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	118143	118913	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	100692	102302	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	110362	114215	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	104822	106072	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00054	7845	9743	+	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00048	19357	21543	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00042	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	48325	49460	-	espR4	99.6	84.4	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	144229	145650	+	espX1	100.0	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	164232	165812	-	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	133441	134733	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	105275	106086	-	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	206256	210504	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00013	115878	118118	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	103862	104818	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	108173	108988	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	106171	107187	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	107184	108176	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	114433	115635	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00027	32354	34375	-	fyuA	100.0	100.0	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	37984	47475	-	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	47563	53670	-	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00058	7015	8802	+	iucA	100.0	94.2	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00058	8803	9750	+	iucB	100.0	95.6	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00058	9750	11492	+	iucC	100.0	96.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00058	11489	12810	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00058	12748	15049	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00004	139036	140076	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00001	219611	220364	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	218044	219687	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	215529	218054	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	214835	215503	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	214190	214777	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00027	53861	54820	-	ybtA	100.0	99.9	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	34506	36083	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	54987	56789	+	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	56776	58578	+	ybtQ	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	59879	61183	+	ybtS	100.0	97.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	36087	36890	-	ybtT	100.0	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	36887	37987	-	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	58571	59851	+	ybtX	100.0	97.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	213525	214115	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID051

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00034	2949	3254	-	afaA	100.0	100.0	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00034	1886	2630	-	afaB-I	100.0	99.6	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00158	3718	4161	-	afaD	100.0	100.0	CAW30800	(afaD) AfaD [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00158	2480	2965	-	afaE-I	100.0	99.8	CAW30801	(afaE-I) AFA-I adhesin [Afa/Dr family (VF0212)] [Escherichia coli O25b:H4 str. FV9863]
contig02639	303	797	+	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig02770	116	571	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig01231	899	1315	+	csgF	99.0	81.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00034	4175	4402	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00158	3167	3340	-	draP	100.0	98.8	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00442	98	1285	+	entC	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00538	177	947	+	entD	100.0	94.3	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00748	1084	1854	+	entD	100.0	99.9	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00442	1295	2634	+	entE	83.2	98.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01069	433	1545	-	entS	89.0	95.3	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00580	92	1990	-	espL1	100.0	96.2	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00285	1971	3221	+	espR1	99.3	94.6	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00169	2908	4047	-	espR3	100.0	96.4	NP_288394	(espR3) Type III secretion system effector espR3 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00365	973	2394	+	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00641	168	1748	+	espX4	100.0	94.9	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00804	637	1448	+	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00052	5564	7972	+	espY4	99.8	89.4	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00127	2810	3625	-	fepC	100.0	97.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig03168	1	672	+	fepC	82.3	99.7	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00127	4611	5627	-	fepD	100.0	97.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00127	3622	4614	-	fepG	100.0	95.3	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00312	2572	3177	-	fimA	100.0	92.1	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00527	1076	1678	+	fimB	100.0	99.7	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00312	1206	1931	-	fimC	100.0	99.2	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00235	1766	2299	-	fimF	100.0	99.1	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00235	1250	1753	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00235	328	1239	-	fimH	100.0	99.0	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00312	1968	2507	-	fimI	100.0	99.4	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00138	37	1887	+	gspD	100.0	94.8	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00138	1887	3380	+	gspE	100.0	94.5	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00138	3380	4579	+	gspF	100.0	94.1	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00138	4620	5075	+	gspG	100.0	96.3	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig03850	233	550	+	gspI	85.5	95.0	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00462	1212	2189	-	gspK	100.0	97.2	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00462	37	897	-	gspL	100.0	95.0	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01035	307	1167	+	gspL	100.0	94.7	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01267	1	366	+	gspM	86.5	95.6	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00562	893	1255	+	gtrA	100.0	92.0	NP_706257	(gtrA) bactoprenol-linked glucose translocase/flippase [LPS (VF0124)] [Shigella flexneri 2a str. 301]
contig00562	1252	2158	+	gtrB	97.5	82.2	NP_706258	(gtrB) bactoprenol glucosyl transferase [LPS (VF0124)] [Shigella flexneri 2a str. 301]
contig00153	659	3733	+	hlyA	100.0	99.9	NP_755445	(hlyA) Hemolysin A [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00153	1	647	+	hlyC	95.8	100.0	NP_755444	(hlyC) Hemolysin C [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00451	901	2337	+	hlyD	100.0	99.9	NP_755449	(hlyD) Hemolysin D [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00167	1596	2825	+	iroD	100.0	99.4	NP_753166	(iroD) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00167	2910	3866	+	iroE	100.0	99.2	NP_753165	(iroE) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00260	300	1247	+	iucB	100.0	100.0	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00260	1247	2989	+	iucC	100.0	99.9	NP_709456	(iucC) aerobactin synthesis protein IucC [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00219	627	2906	+	iutA	100.0	99.6	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00387	728	2404	+	kpsD	100.0	98.0	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00083	271	2793	+	papC	100.0	99.8	NP_755465	(papC) usher protein PapC [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00083	2993	3598	+	papD	100.0	99.8	NP_755464	(papD) chaperone protein PapD [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00083	5361	5891	+	papF	100.0	99.2	NP_755459	(papF) P pilus minor subunit PapF [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00083	5935	6945	+	papG	100.0	99.1	NP_755458	(papG) P pilus tip adhesin PapG [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00083	3635	4216	+	papJ	100.0	99.5	NP_755463	(papJ) P pilus assembly protein PapJ [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00083	4223	4762	+	papK	100.0	99.1	NP_755461	(papK) P pilus minor subunit PapK [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00090	6059	6610	-	papX	100.0	100.0	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00041	799	1937	-	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig01982	511	1005	+	shuX	100.0	96.2	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00082	1	3871	+	vat	93.7	99.7	NP_752330	(vat) Haemoglobin protease [Tsh (VF0233)] [Escherichia coli CFT073]
contig02336	340	884	+	yagY/ecpB	81.5	98.5	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig03003	177	721	+	yagY/ecpB	81.5	98.0	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00625	578	2140	+	ybtQ	86.7	99.9	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig01751	292	1095	-	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00633	687	1967	-	ybtX	100.0	97.6	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00956	1	497	-	ykgK/ecpR	84.1	99.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID052

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00015	53014	54442	+	aslA	100.0	97.3	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00002	110304	111296	-	chuU	100.0	98.6	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00002	109537	110337	-	chuV	100.0	98.4	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00002	112475	113812	-	chuW	100.0	96.8	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00002	111345	111968	-	chuY	100.0	97.0	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00039	10912	11367	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00039	9507	10157	-	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00039	8672	9088	-	csgF	99.0	81.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00039	7812	8645	-	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00009	84305	85051	-	entA	100.0	95.8	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	85051	85908	-	entB	100.0	97.2	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	87542	88729	-	entC	100.0	98.2	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	103186	103956	+	entD	100.0	93.8	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	85922	87532	-	entE	100.0	97.6	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	95405	99258	-	entF	99.3	95.9	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	89866	91116	-	entS	100.0	95.7	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003	99918	101816	-	espL1	100.0	96.4	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00010	7968	10154	-	espL4	100.0	97.1	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00068	14349	15599	-	espR1	99.3	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	120856	122277	+	espX1	100.0	94.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	84366	86378	-	espX2	100.0	96.7	NP_286562	(espX2) Type III secretion system effector EspX2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00010	42382	43962	+	espX4	100.0	94.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00010	73473	74765	-	espX5	100.0	95.6	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	81432	82151	-	espY1	95.6	88.6	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	64452	65021	-	espY2	100.0	94.2	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	120255	121826	-	espY3	100.0	95.4	NP_286160	(espY3) Type III secretion system effector EspY3 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	39417	41825	+	espY4	100.0	92.7	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00040	3659	7900	-	fdeC	99.8	91.3	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00009	100921	103161	+	fepA	100.0	97.2	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	88906	89862	+	fepB	100.0	97.0	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	93217	94032	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	91215	92231	+	fepD	100.0	95.7	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	92228	93220	+	fepG	100.0	95.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	99476	100678	-	fes	100.0	97.4	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	38364	39194	-	gspC	100.0	95.4	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	36274	38124	-	gspD	100.0	95.6	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	34781	36274	-	gspE	100.0	95.3	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	33582	34781	-	gspF	100.0	91.5	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	33086	33541	-	gspG	100.0	97.4	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	32519	33049	-	gspH	100.0	96.2	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	32151	32522	-	gspI	100.0	94.9	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	31549	32118	-	gspJ	100.0	94.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	30575	31552	-	gspK	100.0	96.7	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	29400	30260	-	gspL	100.0	95.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	28863	29284	-	gspM	99.8	93.4	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00058	15698	16927	+	iroD	100.0	99.6	NP_753166	(iroD) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00058	17012	17969	+	iroE	100.0	99.0	NP_753165	(iroE) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00001	14169	15845	+	kpsD	100.0	99.5	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00001	26913	27689	-	kpsM	100.0	94.1	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00012	26051	27103	-	ompA	100.0	95.2	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00135	961	1512	+	papX	100.0	97.5	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00002	115430	117412	+	shuA	100.0	98.8	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00002	117461	118489	+	shuS	100.0	96.8	YP_405020	(shuS) heme/hemoglobin transport protein ShuS [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00002	113832	114824	-	shuT	100.0	97.8	YP_405017	(shuT) periplasmic binding protein ShuT [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00002	111968	112462	-	shuX	100.0	96.6	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00040	23310	24063	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00040	21743	23386	+	yagW/ecpD	100.0	98.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00040	19228	21753	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00040	18534	19202	+	yagY/ecpB	100.0	97.6	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00040	17889	18476	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00040	17225	17815	+	ykgK/ecpR	100.0	98.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID057

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00076	9106	9561	-	csgB	99.8	84.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00076	10315	10965	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00076	11384	11800	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00076	11827	12660	+	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00028	35282	36028	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00028	36028	36885	-	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00028	38519	39706	-	entC	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00028	54350	55120	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00028	36899	38509	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00028	46593	50422	-	entF	98.7	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00028	41029	42279	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00010	11533	13401	-	espL1	98.4	95.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00047	24866	25921	+	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00021	50824	52244	+	espX1	99.9	94.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015	55538	57118	-	espX4	99.9	93.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015	24726	26018	+	espX5	100.0	95.7	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00012	43044	47285	-	fdeC	99.8	92.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00028	52085	54325	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00028	40069	41025	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00028	44380	45195	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00028	42378	43394	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00028	43391	44383	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00028	50640	51842	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00014	97608	98213	-	fimA	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00054	1113	1715	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	96242	96967	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	93539	96175	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00054	39	635	-	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	92999	93532	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	92483	92986	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	91561	92472	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	97004	97543	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	144864	145694	-	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	142774	144624	-	gspD	100.0	97.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	141281	142774	-	gspE	100.0	97.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	140082	141281	-	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	139586	140041	-	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	139019	139549	-	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	138651	139022	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	138049	138618	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	137075	138052	-	gspK	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	135900	136760	-	gspL	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	135362	135784	-	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	104083	105135	-	ompA	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00012	56391	57144	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00012	54824	56467	+	yagW/ecpD	100.0	98.6	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00012	52309	54834	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00012	51615	52283	+	yagY/ecpB	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00012	50970	51557	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00012	50305	50895	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID058

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00028	619	2047	+	aslA	100.0	92.9	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00207	188	643	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00207	1398	2048	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00207	2467	2883	+	csgF	99.0	81.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00207	2910	3743	+	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00807	1	1533	+	entE	95.2	95.1	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01126	1	1353	+	entE	84.0	94.9	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00258	371	1791	+	espX1	99.9	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00671	360	1940	-	espX4	100.0	96.5	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00134	2697	3989	-	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00933	296	1118	+	espY1	100.0	85.9	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00837	592	1548	-	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00545	740	1756	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00156	4587	5192	-	fimA	100.0	95.5	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00005	23472	24074	+	fimB	100.0	97.7	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00156	3222	3947	-	fimC	100.0	99.2	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00156	519	3155	-	fimD	100.0	98.9	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00005	24552	25148	+	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00156	1	512	-	fimF	95.9	99.0	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00446	1	509	+	fimF	95.3	97.5	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00446	522	1025	+	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00446	1036	1947	+	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00156	3984	4522	-	fimI	99.8	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00453	52	888	+	fliG	84.3	80.2	YP_001006742	(fliG) flagellar motor switch protein G [Flagella (VF0394)] [Yersinia enterocolitica subsp. enterocolitica 8081]
contig00017	8334	10355	+	fyuA	100.0	99.7	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	17541	18371	+	gspC	100.0	95.4	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	18611	20461	+	gspD	100.0	97.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	20461	21954	+	gspE	100.0	96.5	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	21954	23153	+	gspF	100.0	96.1	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	23194	23649	+	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	23686	24216	+	gspH	100.0	95.3	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	24213	24584	+	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	24617	25186	+	gspJ	100.0	96.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	25183	26160	+	gspK	100.0	96.7	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	26475	27335	+	gspL	100.0	97.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	9600	15713	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00060	2881	3921	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00001	8272	9025	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	6705	8348	+	yagW/ecpD	100.0	99.0	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	4190	6715	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	3496	4164	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	2851	3438	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006	8450	9409	+	ybtA	100.0	99.4	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	6626	8203	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	6481	8283	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	4692	6494	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	2087	3391	-	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	5819	6622	+	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	4722	5822	+	ybtU	100.0	99.2	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	3419	4699	-	ybtX	100.0	99.8	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	2186	2776	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID066

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00005	187988	188443	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005	189197	189847	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005	190266	190682	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005	190709	191542	+	csgG	100.0	83.0	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00013	99473	100219	-	entA	100.0	95.5	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	100219	101076	-	entB	100.0	97.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	102710	103897	-	entC	100.0	97.6	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	118541	119311	+	entD	100.0	94.3	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	101090	102700	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	110784	114613	-	entF	98.7	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	105220	106470	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	275319	277218	-	espL1	100.0	95.7	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00033	24925	25980	+	espR1	83.8	94.1	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00012	18826	20246	+	espX1	99.9	95.8	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00009	60834	62414	+	espX4	99.9	93.0	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00009	91971	93263	-	espX5	100.0	95.9	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00024	38523	42771	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00013	116276	118516	+	fepA	100.0	97.1	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	104260	105216	+	fepB	100.0	97.1	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	108571	109386	+	fepC	100.0	97.2	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	106569	107585	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	107582	108574	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	114831	116033	-	fes	100.0	96.5	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00012	142063	142668	-	fimA	100.0	92.9	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	35938	36540	+	fimB	100.0	98.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00012	140697	141422	-	fimC	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00012	137994	140630	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	37018	37614	+	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00012	137454	137987	-	fimF	100.0	98.3	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00012	136938	137441	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00012	136016	136927	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00012	141459	141998	-	fimI	100.0	99.1	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00001	19552	21573	-	fyuA	100.0	99.9	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00002	172124	172954	+	gspC	100.0	95.2	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	173194	175044	+	gspD	100.0	97.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	175044	176537	+	gspE	100.0	96.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	176537	177736	+	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	177777	178232	+	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	178269	178799	+	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	178796	179167	+	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	179200	179769	+	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	179766	180743	+	gspK	100.0	97.8	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	181058	181918	+	gspL	100.0	97.3	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	182034	182456	+	gspM	100.0	95.0	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	25183	34674	-	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	34762	40869	-	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00018	77079	78131	-	ompA	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00024	51877	52630	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00024	50310	51953	+	yagW/ecpD	100.0	98.7	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00024	47795	50320	+	yagX/ecpC	100.0	98.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00024	47101	47769	+	yagY/ecpB	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00024	46456	47043	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	41060	42019	-	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	21705	23282	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	42186	43988	+	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	43975	45777	+	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	47078	48382	+	ybtS	100.0	99.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	23286	24089	-	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	24086	25186	-	ybtU	100.0	99.5	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	45770	47050	+	ybtX	100.0	99.8	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	45791	46381	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID070

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00016	49279	50707	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00056	6303	6758	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00056	4898	5548	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00056	4063	4479	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00056	3203	4036	-	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00015	68993	69739	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	69739	70596	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	72230	73417	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	88061	88831	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	70610	72220	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	80280	84133	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	74740	75990	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00002	204355	206254	-	espL1	100.0	97.5	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	7262	9448	-	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00069	56	1109	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00032	46249	47670	+	espX1	100.0	93.3	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	37664	39244	+	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	68743	70035	-	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00032	7294	8104	-	espY1	99.7	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00026	28754	33002	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00015	85796	88036	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	73780	74736	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	78091	78906	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	76089	77105	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	77102	78094	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	84351	85553	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00053	25238	25849	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00059	1110	1712	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	23872	24597	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	21169	23805	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00059	39	633	-	fimE	99.7	99.3	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	20629	21162	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	20113	20616	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	19191	20102	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	24634	25173	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00006	98307	99137	-	gspC	100.0	95.0	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	96217	98067	-	gspD	100.0	97.3	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	94724	96217	-	gspE	100.0	96.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	93525	94724	-	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	93029	93484	-	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	92462	92992	-	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	92094	92465	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	91492	92061	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	90518	91495	-	gspK	100.0	97.8	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	89343	90203	-	gspL	100.0	97.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	88805	89227	-	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00071	7016	8803	+	iucA	100.0	94.2	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00071	8804	9751	+	iucB	100.0	95.6	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00071	9751	11493	+	iucC	100.0	96.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00071	11490	12811	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00071	12749	15050	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00004	75969	77009	-	ompA	100.0	98.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00026	42110	42863	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00026	40543	42186	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00026	38028	40553	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00026	37334	38002	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00026	36689	37276	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00026	36024	36614	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID073

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00015	49877	51305	+	aslA	100.0	94.0	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00028	45439	46431	-	chuU	100.0	97.8	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00028	44672	45472	-	chuV	100.0	98.1	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00028	47610	48947	-	chuW	100.0	95.8	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00028	46480	47103	-	chuY	100.0	95.2	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00074	244	1077	+	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00031	31829	32575	-	entA	100.0	95.2	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00031	32575	33432	-	entB	100.0	97.7	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00031	35066	36253	-	entC	100.0	98.0	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00031	50711	51481	+	entD	100.0	94.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00031	33446	35056	-	entE	100.0	95.6	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00031	42930	46783	-	entF	99.2	95.5	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00031	37390	38640	-	entS	100.0	96.1	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00035	18791	20689	+	espL1	100.0	98.7	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00057	17740	19926	+	espL4	100.0	97.8	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	219334	220473	-	espR3	100.0	94.5	NP_288394	(espR3) Type III secretion system effector espR3 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	221297	222406	-	espR4	97.3	84.4	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00026	56526	57947	+	espX1	100.0	96.9	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00069	1	1275	-	espX4	80.7	96.5	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00026	17117	17839	-	espY1	96.0	93.2	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00026	153	722	-	espY2	100.0	98.6	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	32205	33764	-	espY3	99.2	98.7	NP_286160	(espY3) Type III secretion system effector EspY3 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00041	27499	31737	-	fdeC	99.7	93.3	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00031	48446	50686	+	fepA	100.0	96.5	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00031	36430	37386	+	fepB	100.0	97.8	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00031	40741	41556	+	fepC	100.0	97.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00031	38739	39755	+	fepD	100.0	96.7	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00031	39752	40744	+	fepG	100.0	94.7	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00031	47001	48203	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00081	15577	16188	-	fimA	100.0	88.4	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00066	1120	1722	-	fimB	100.0	97.7	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00081	14211	14936	-	fimC	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00081	11508	14144	-	fimD	100.0	98.4	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00066	49	643	-	fimE	99.7	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00081	10968	11501	-	fimF	100.0	97.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00081	10452	10955	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00081	9530	10441	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00081	14973	15512	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00049	30592	32613	+	fyuA	100.0	99.5	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	17492	26983	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	11297	17404	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00098	2142	3929	+	iucA	100.0	100.0	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00098	3930	4877	+	iucB	100.0	99.9	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00098	4877	6619	+	iucC	100.0	99.9	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00098	6616	7953	+	iucD	100.0	99.9	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00098	7875	10154	+	iutA	100.0	99.7	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00032	15561	16613	-	ompA	100.0	95.2	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00028	50564	52546	+	shuA	100.0	99.3	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00028	52595	53623	+	shuS	100.0	98.5	YP_405020	(shuS) heme/hemoglobin transport protein ShuS [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00028	48967	49959	-	shuT	100.0	97.6	YP_405017	(shuT) periplasmic binding protein ShuT [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00028	47103	47597	-	shuX	100.0	98.2	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00049	10147	11106	+	ybtA	100.0	99.4	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	28884	30461	+	ybtE	100.0	99.9	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	8178	9980	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	6389	8191	-	ybtQ	100.0	99.6	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	3784	5088	-	ybtS	100.0	99.5	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	28077	28880	+	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	26980	28080	+	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	5116	6396	-	ybtX	100.0	99.6	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]

ID081

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00016	49279	50707	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00035	40481	40936	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00035	41691	42341	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00035	42760	43176	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00035	43203	44036	+	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012	77381	78127	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	78127	78984	-	entB	100.0	98.0	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	80618	81805	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	96449	97219	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	78998	80608	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	88668	92521	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	83128	84378	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00057	18427	20325	+	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00056	19357	21543	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00044	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	48323	49458	-	espR4	99.6	84.4	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	144224	145645	+	espX1	100.0	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00019	8865	10445	+	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00019	39944	41236	-	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	105270	106081	-	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	58929	63177	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00012	94184	96424	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	82168	83124	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	86479	87294	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	84477	85493	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	85490	86482	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	92739	93941	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00020	46364	48385	-	fyuA	100.0	100.0	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	51994	61485	-	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	61573	67680	-	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00072	7015	8802	+	iucA	100.0	94.2	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00072	8803	9750	+	iucB	100.0	95.6	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00072	9750	11492	+	iucC	100.0	96.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00072	11489	12810	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00072	12748	15049	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00004	103766	104806	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00017	72284	73037	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	70717	72360	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	68202	70727	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	67508	68176	+	yagY/ecpB	100.0	97.9	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	66863	67450	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00020	67871	68830	-	ybtA	100.0	99.9	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	48516	50093	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	68997	70799	+	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	70786	72588	+	ybtQ	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	73889	75193	+	ybtS	100.0	97.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	50097	50900	-	ybtT	100.0	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	50897	51997	-	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	72581	73861	+	ybtX	100.0	97.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	66198	66788	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID096I

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00147	4955	5700	+	entA	99.2	80.4	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00147	4094	4945	+	entB	99.2	81.7	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00300	127	898	+	fepC	94.6	80.7	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	58424	60445	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	45324	54815	+	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	39129	45236	+	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	18165	19235	-	ompA	100.0	83.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00142	10793	11546	+	yagV/ecpE	99.7	85.4	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00142	9224	10867	+	yagW/ecpD	100.0	88.7	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00142	6709	9234	+	yagX/ecpC	100.0	87.3	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00142	6015	6683	+	yagY/ecpB	100.0	87.9	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00142	5368	5951	+	yagZ/ecpA	99.3	90.1	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	37979	38938	+	ybtA	100.0	99.9	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	56716	58293	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	36010	37812	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	34221	36023	-	ybtQ	100.0	99.9	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	31616	32920	-	ybtS	100.0	97.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	55909	56712	+	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	54812	55912	+	ybtU	100.0	99.6	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	32948	34228	-	ybtX	100.0	97.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00142	4713	5293	+	ykgK/ecpR	98.3	86.2	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID098

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00083	2493	3921	+	aslA	100.0	97.4	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00053	25876	26904	+	chuS	100.0	98.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00053	22247	23239	-	chuT	100.0	99.4	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00053	18719	19711	-	chuU	100.0	99.1	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00053	17952	18752	-	chuV	100.0	98.4	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00053	20890	22227	-	chuW	100.0	97.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00053	19760	20383	-	chuY	100.0	96.3	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00045	28463	31507	-	cnf1	100.0	99.9	CAA50007	(cnf1) cytotoxic necrotizing factor 1 [CNF-1 (VF0240)] [Escherichia coli str. E-B35]
contig00023	46133	46588	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00131	67	717	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00131	1136	1552	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00131	1579	2412	+	csgG	100.0	82.8	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00002	30548	31294	-	entA	100.0	96.4	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	31294	32151	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	33785	34972	-	entC	100.0	98.4	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	49429	50199	+	entD	100.0	93.9	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	32165	33775	-	entE	100.0	96.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	41648	45501	-	entF	99.3	96.3	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	36109	37359	-	entS	100.0	96.3	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00004	472	2370	-	espL1	100.0	96.0	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	49067	50317	+	espR1	99.3	94.7	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00042	21241	22821	+	espX4	100.0	96.0	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00074	15179	15927	+	espY1	99.5	94.4	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00059	7955	8524	+	espY2	100.0	94.0	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00043	1	2266	+	espY4	93.9	88.8	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00012	44495	48736	-	fdeC	99.8	92.0	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00002	47164	49404	+	fepA	100.0	97.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	35149	36105	+	fepB	100.0	98.2	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	39460	40275	+	fepC	100.0	97.7	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	37458	38474	+	fepD	100.0	96.5	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	38471	39463	+	fepG	100.0	94.5	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	45719	46921	-	fes	100.0	97.0	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00146	7502	8107	-	fimA	100.0	92.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00278	709	1311	+	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00146	6136	6861	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00146	3433	6069	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00278	1789	2385	+	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00146	2893	3426	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00146	2377	2880	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00146	1455	2366	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00146	6898	7437	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00157	1	1741	+	fyuA	86.1	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00055	17448	18278	+	gspC	100.0	94.7	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00055	18518	20368	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00055	20368	21861	+	gspE	100.0	94.6	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00055	21861	23060	+	gspF	100.0	94.5	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00055	23101	23556	+	gspG	100.0	96.3	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00055	23593	24123	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00055	24120	24491	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00055	24524	25093	+	gspJ	100.0	94.6	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00055	25090	26067	+	gspK	100.0	96.5	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00055	26382	27242	+	gspL	100.0	95.0	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00055	27358	27779	+	gspM	99.8	97.4	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00127	5764	8838	+	hlyA	100.0	98.6	NP_755445	(hlyA) Hemolysin A [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00127	8909	10812	+	hlyB	89.6	99.1	NP_755448	(hlyB) Hemolysin B [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00127	5078	5752	+	hlyC	100.0	100.0	NP_755444	(hlyC) Hemolysin C [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00045	32453	33889	-	hlyD	100.0	99.9	NP_755449	(hlyD) Hemolysin D [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00099	7302	9089	+	iucA	100.0	94.3	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00099	9090	10037	+	iucB	100.0	95.7	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00099	10037	11779	+	iucC	100.0	96.1	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00099	11776	13097	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00099	13035	15336	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00085	12599	14275	-	kpsD	100.0	97.9	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00055	28837	29613	+	kpsM	100.0	95.1	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00010	78486	79333	-	ompA	81.5	97.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00045	8346	8660	-	papB	100.0	99.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00045	4365	6887	-	papC	100.0	99.7	NP_755465	(papC) usher protein PapC [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00045	3560	4165	-	papD	100.0	99.8	NP_755464	(papD) chaperone protein PapD [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00045	1848	2387	-	papE	100.0	100.0	NP_755460	(papE) P pilus minor subunit PapE [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00045	1273	1803	-	papF	100.0	100.0	NP_755459	(papF) P pilus minor subunit PapF [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00045	219	1229	-	papG	100.0	99.1	NP_755458	(papG) P pilus tip adhesin PapG [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00045	6934	7521	-	papH	100.0	98.0	NP_755466	(papH) P pilus termination subunit PapH [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00045	9065	9298	+	papI	100.0	94.0	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00045	2942	3523	-	papJ	100.0	98.6	NP_755463	(papJ) P pilus assembly protein PapJ [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00045	2396	2935	-	papK	100.0	99.3	NP_755461	(papK) P pilus minor subunit PapK [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00458	173	724	+	papX	100.0	97.5	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00053	23845	25827	+	shuA	100.0	98.0	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00053	20383	20877	-	shuX	100.0	96.6	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00012	64148	64901	+	yagV/ecpE	99.7	98.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00012	62581	64224	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00012	60066	62591	+	yagX/ecpC	100.0	98.5	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00012	59372	60040	+	yagY/ecpB	100.0	99.0	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00012	58727	59314	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00329	353	1997	+	ybtQ	91.2	99.9	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00227	2036	3183	-	ybtS	88.0	97.7	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00440	1	663	-	ybtT	82.5	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00467	1	1046	-	ybtX	81.7	99.4	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00488	27	1055	-	ybtX	80.3	97.3	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00012	58062	58652	+	ykgK/ecpR	100.0	99.7	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID099

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00032	15069	16497	+	aslA	100.0	92.9	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00001	128600	129055	+	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	127195	127845	-	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	126360	126776	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	125500	126333	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00036	28650	29396	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00036	29396	30253	-	entB	100.0	98.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00036	31887	33074	-	entC	100.0	98.3	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00036	47718	48488	+	entD	100.0	95.1	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00036	30267	31877	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00036	39937	43790	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00036	34397	35647	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00086	125	1545	+	espX1	99.9	95.3	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00019	18898	20478	+	espX4	99.9	94.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00019	49982	51274	-	espX5	100.0	97.0	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	94198	94994	-	espY1	99.9	88.7	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00084	24	4272	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00036	45453	47693	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00036	33437	34393	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00036	37748	38563	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00036	35746	36762	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00036	36759	37751	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00036	44008	45210	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00073	12316	12927	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00082	1110	1712	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00073	10950	11675	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00073	8247	10883	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00082	39	633	-	fimE	99.7	99.3	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00073	7707	8240	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00073	7191	7694	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00073	6269	7180	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00073	11712	12251	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00001	54588	55628	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00068	5970	6723	+	yagV/ecpE	99.7	97.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00068	4400	6046	+	yagW/ecpD	100.0	98.8	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00068	1886	4410	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00068	1192	1860	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00068	547	1134	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID24

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00022	49173	50601	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00032	8088	8543	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	6681	7331	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	5846	6262	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	4986	5819	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00038	18008	18754	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	18754	19611	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	21245	22432	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	37076	37846	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	19625	21235	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	29295	33148	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	23755	25005	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00025	23930	25830	+	espL1	100.0	97.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015	102829	105015	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00040	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	69187	70608	-	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015	73033	74613	-	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015	42242	43534	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	108754	109565	+	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	265193	269441	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00038	34811	37051	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	22795	23751	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	27106	27921	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	25104	26120	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	26117	27109	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00038	33366	34568	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00048	25238	25849	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00048	23872	24597	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00048	21169	23805	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00048	20629	21162	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00048	20113	20616	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00048	19191	20102	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00048	24634	25173	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00031	30503	32524	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	17403	26894	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	11208	17315	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00002	219469	220509	-	ompA	100.0	98.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00001	278552	279305	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	276985	278628	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	274470	276995	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	273776	274444	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	273131	273718	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	10058	11017	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	28795	30372	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	8089	9891	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	6300	8102	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	3695	4999	-	ybtS	100.0	99.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	27988	28791	+	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	26891	27991	+	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	5027	6307	-	ybtX	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	272466	273056	+	ykgK/ecpR	100.0	96.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

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Multi-Locus Sequence Typing (MLST)

Symbol	Meaning
~	novel full length allele similar to match
?	partial match to known allele
-	allele missing

	Scheme	ST	1	2	3	4	5	6	7
ID005zero	ecoli	1193	adk(14)	fumC(14)	gyrB(10)	icd(200)	mdh(17)	purA(7)	recA(10)
ID008	-	-
ID009	kpneumoniae	489	gapA(18)	infB(22)	mdh(26)	pgi(71)	phoE(98)	rpoB(52)	tonB(51)
ID011	ecoli	10	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
ID013	ecoli	-	adk(85)	fumC(88)	gyrB(78)	icd(29)	mdh(910?)	purA(58)	recA(725?)
ID014at24	senterica	-	aroC(~622)	dnaN(~603)	hemD(554)	hisD(836)	purE(~690)	sucA(281?)	thrA(695?)
ID015at48	ecoli	448	adk(6)	fumC(6)	gyrB(5)	icd(16)	mdh(11)	purA(8)	recA(7)
ID015HW	ecoli	448	adk(6)	fumC(6)	gyrB(5)	icd(16)	mdh(11)	purA(8)	recA(7)
ID016at24	ecoli	656	adk(10)	fumC(7)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
ID017at48	ecoli	656	adk(10)	fumC(7)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
ID018at24	ecoli	1193	adk(14)	fumC(14)	gyrB(10)	icd(200)	mdh(17)	purA(7)	recA(10)
ID020at24	cfreundii	-	aspC(171)	clpX(193)	fadD(112)	mdh(172)	arcA(111)	dnaG(84)	lysP(~101)
ID021at24	ecoli	6438	adk(6)	fumC(11)	gyrB(103)	icd(113)	mdh(8)	purA(1)	recA(2)
ID025I	ecoli	656	adk(10)	fumC(7)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
ID025II	ecoli	656	adk(10)	fumC(7)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
ID025III	-	-
ID026	ecoli	656	adk(10)	fumC(7)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
ID027	ecoli	656	adk(10)	fumC(7)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
ID031	ecoli	998	adk(13)	fumC(52)	gyrB(156)	icd(14)	mdh(17)	purA(25)	recA(17)
ID032I	ecoli	131	adk(53)	fumC(40)	gyrB(47)	icd(13)	mdh(36)	purA(28)	recA(29)
ID033I	ecoli	206	adk(6)	fumC(7)	gyrB(5)	icd(1)	mdh(8)	purA(18)	recA(2)
ID034I	ecoli	656	adk(10)	fumC(7)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
ID034II	ecoli	656	adk(10)	fumC(7)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
ID037	ecoli	541	adk(111)	fumC(23)	gyrB(109)	icd(8)	mdh(8)	purA(8)	recA(2)
ID043I	ecoli	38	adk(4)	fumC(26)	gyrB(2)	icd(25)	mdh(5)	purA(5)	recA(19)
ID045	ecoli	847	adk(6)	fumC(6)	gyrB(5)	icd(26)	mdh(9)	purA(13)	recA(98)
ID047	ecoli	405	adk(35)	fumC(37)	gyrB(29)	icd(25)	mdh(4)	purA(5)	recA(73)
ID050	ecoli	1284	adk(10)	fumC(4)	gyrB(4)	icd(8)	mdh(8)	purA(13)	recA(73)
ID051	ecoli	-	adk(~6)	fumC(88)	gyrB(983?)	icd(1250?)	mdh(208?)	purA(772?)	recA(62)
ID052	ecoli	349	adk(34)	fumC(36)	gyrB(39)	icd(87)	mdh(67)	purA(16)	recA(4)
ID057	ecoli	3580	adk(6)	fumC(65)	gyrB(344)	icd(1)	mdh(11)	purA(13)	recA(6)
ID058	ecoli	-	adk(6)	fumC(1509?)	gyrB(979?)	icd(8)	mdh(8)	purA(696?)	recA(2)
ID066	ecoli	224	adk(6)	fumC(4)	gyrB(33)	icd(16)	mdh(11)	purA(8)	recA(6)
ID070	ecoli	44	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(7)
ID073	ecoli	3036	adk(207)	fumC(297)	gyrB(260)	icd(254)	mdh(1)	purA(261)	recA(2)
ID081	ecoli	1284	adk(10)	fumC(4)	gyrB(4)	icd(8)	mdh(8)	purA(13)	recA(73)
ID096I	kpneumoniae	39	gapA(2)	infB(1)	mdh(2)	pgi(4)	phoE(9)	rpoB(1)	tonB(14)
ID098	ecoli	648	adk(92)	fumC(4)	gyrB(87)	icd(96)	mdh(70)	purA(58)	recA(2)
ID099	ecoli	206	adk(6)	fumC(7)	gyrB(5)	icd(1)	mdh(8)	purA(18)	recA(2)
ID24	ecoli	656	adk(10)	fumC(7)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)

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Pangenome Analysis

Pangenome genes summary

Genes	Description	Number
Core genes	(99% <= strains <= 100%)	0
Soft core genes	(95% <= strains < 99%)	129
Shell genes	(15% <= strains < 95%)	6057
Cloud genes	(0% <= strains < 15%)	22414
Total genes	(0% <= strains <= 100%)	28600

Schematic representation of genes presence (color) or absence (blank) between samples:

Pangenome tree based on presence/absence of accessory genes representation

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)

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Pangenome tree based on core genome alignment representation

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)

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Insertion sequence characterization

Field	Description
Region	Numeric code given to insertion sequence (IS)
Orientation	The orientation of IS position: Either forward (F) or reverse (F)
X-cordinates	The left coordinate of the position
Y-coordinates	The right coordinate of the position
Gap	The distance between the x and y coordinates
CallType	Describes whether a position hit is novel (not in reference) or known (in the reference)
LeftGene	Locus tag ID of the gene closest to the left side of the IS position
LeftGeneDescription	Description of the gene feature from the left side of the IS position. By default this is the product position
RightGene	Locus tag ID of the gene closest to the right side of the IS position
RightGeneDescription	Description of the gene feature from the right side of the IS position. By default this is the product position

Select the sample

ID005zero

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	1950788	1950789	novel	b4403	putative rRNA methyltransferase	b1867	putative hydrolase

ID009

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	1994808	1994814	-6	novel	b1914	DNA-binding transcriptional activator UvrY	b1914	DNA-binding transcriptional activator UvrY

ID013

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	FALSE	2481118	2481137	19	novel*	b2367	tripartite efflux pump membrane subunit EmrY	b2367	tripartite efflux pump membrane subunit EmrY

ID014at24

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	1040587	1040588	novel	b4403	putative rRNA methyltransferase	b0980	periplasmic phosphoanhydride phosphatase/multiple inositol-polyphosphate phosphatase

ID015HW

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	F	2192272	2192276	-4	novel	b2111	putative fimbrial protein YehD	b2112	DUF2574 domain-containing protein YehE
region_1	R	-1	1207440	1207441	novel	b4403	putative rRNA methyltransferase	b1153	e14 prophage; conserved protein YmfQ
region_2	R	-1	2471880	2471881	novel	b4403	putative rRNA methyltransferase	b2355	CPS-53 (KpLE1) prophage; putative uncharacterized protein YfdL

ID015at48

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	F	2192277	2192301	24	novel*	b2111	putative fimbrial protein YehD	b2112	DUF2574 domain-containing protein YehE
region_1	R	-1	1207440	1207441	novel	b4403	putative rRNA methyltransferase	b1153	e14 prophage; conserved protein YmfQ
region_2	R	-1	2471880	2471881	novel	b4403	putative rRNA methyltransferase	b2355	CPS-53 (KpLE1) prophage; putative uncharacterized protein YfdL

ID016at24

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	FALSE	2481107	2481118	-11	novel	b2367	tripartite efflux pump membrane subunit EmrY	b2367	tripartite efflux pump membrane subunit EmrY

ID017at48

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	FALSE	2481107	2481118	-11	novel	b2367	tripartite efflux pump membrane subunit EmrY	b2367	tripartite efflux pump membrane subunit EmrY

ID018at24

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	1950795	1950796	novel	b4403	putative rRNA methyltransferase	b1867	putative hydrolase

ID020at24

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	2009793	2009794	novel	b4403	putative rRNA methyltransferase	b1931	putative SOS response-associated peptidase YedK

ID025III

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	FALSE	2481079	2481166	87	novel*	b2367	tripartite efflux pump membrane subunit EmrY	b2367	tripartite efflux pump membrane subunit EmrY

ID025II

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	FALSE	2481107	2481118	-11	novel	b2367	tripartite efflux pump membrane subunit EmrY	b2367	tripartite efflux pump membrane subunit EmrY

ID025I

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	FALSE	2481107	2481118	-11	novel	b2367	tripartite efflux pump membrane subunit EmrY	b2367	tripartite efflux pump membrane subunit EmrY

ID026

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	FALSE	2481107	2481118	-11	novel	b2367	tripartite efflux pump membrane subunit EmrY	b2367	tripartite efflux pump membrane subunit EmrY

ID027

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	FALSE	2481107	2481118	-11	novel	b2367	tripartite efflux pump membrane subunit EmrY	b2367	tripartite efflux pump membrane subunit EmrY

ID032I

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	3861012	3861013	novel	b4403	putative rRNA methyltransferase	b3680	putative DNA-binding transcriptional regulator YidL
region_2	R	-1	3864565	3864566	novel	b4403	putative rRNA methyltransferase	b3684	putative DNA-binding transcriptional regulator YidP

ID034II

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	FALSE	2481107	2481118	-11	novel	b2367	tripartite efflux pump membrane subunit EmrY	b2367	tripartite efflux pump membrane subunit EmrY

ID034I

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	FALSE	2481107	2481118	-11	novel	b2367	tripartite efflux pump membrane subunit EmrY	b2367	tripartite efflux pump membrane subunit EmrY

ID043I

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	2082125	2082126	novel	b4403	putative rRNA methyltransferase	b2010	D-alanyl-D-alanine carboxypeptidase DacD

ID047

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	1427116	1427117	novel	b4403	putative rRNA methyltransferase	b1368	Rac prophage; putative prophage tail length tape measure domain-containing protein YnaA

ID050

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	2060961	2060970	-9	novel	b1987	DNA-binding transcriptional activator Cbl	b1988	DNA-binding transcriptional dual regulator Nac
region_2	F	2990166	2990175	-9	novel	b2849	protein YqeK	b2849	protein YqeK
region_3	F	3414054	3414067	-13	novel	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE
region_4	R	3838044	3838053	-9	novel	b3659	putative arabinose exporter	b3659	putative arabinose exporter

ID058

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	F	2256055	2256065	10	novel	b2163	putative DNA-binding transcriptional regulator YeiL	b2164	putative pseudouridine transporter
region_1	R	2996594	2997421	827	novel*	b2860	IS2 insertion element protein InsB	b2861	IS2 insertion element repressor InsA

ID070

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	735041	735067	26	novel*	b0703	conserved protein, rhs-like YbfO	b0703	conserved protein, rhs-like YbfO
region_2	F	2860407	2860413	-6	novel	b2734	phosphoprotein phosphatase 2	b2734	phosphoprotein phosphatase 2

ID081

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	F	1362334	1362344	-10	novel	b1299	DNA-binding transcriptional repressor PuuR	b1299	DNA-binding transcriptional repressor PuuR
region_2	R	1474974	1474982	-8	novel	b1406	pyridoxine 4-dehydrogenase	b1406	pyridoxine 4-dehydrogenase
region_3	F	3414054	3414067	-13	novel	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE

ID096I

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	361882	361883	novel	b4403	putative rRNA methyltransferase	b0343	lactose permease

ID098

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	2045798	2045799	novel	b4403	putative rRNA methyltransferase	b1978	inverse autotransporter adhesin
region_2	R	-1	4537613	4537614	novel	b4403	putative rRNA methyltransferase	b4310	N-acetylneuraminate mutarotase

ID24

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	FALSE	2481107	2481118	-11	novel	b2367	tripartite efflux pump membrane subunit EmrY	b2367	tripartite efflux pump membrane subunit EmrY

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Citations and Bibliography

If you have used rMAP, please cite:

Sserwadda, I., & Mboowa, G. (2021). rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data. Microbial genomics, 7(6), 10.1099/mgen.0.000583. https://doi.org/10.1099/mgen.0.000583

The philosophy of rMAP was built on the foundation of already pre-existing tools. As a token of gratitude to the authors of those numerous tools, please also cite:

• ABRicate, T. Seemann
• AmrfinderPlus, Feldgarden M. et al., 2019
• Any2fasta, T. Seemann
• Assembly-stats, Sanger Pathogens
• Biopython.convert, biopython.org
• Bwa, Li H. et al., 2009
• Bmge, Criscuolo et al., 2010
• Cairosvg, cairosvg.org
• Fasttree, M.N. Price et al., 2009
• Fastqc, Andrews S., 2010
• Freebayes, Garrison E. et al., 2012
• ISmapper, [Hawkey J. et al., 2015
• Iqtree, Nguyen L. et al., 2015
• Kleborate, Holt KE, 2020
• Mafft, Katoh K. et L., 2013
• Megahit, Li D. et al., 2015
• Mlst, T. Seemann
• Multiqc, Ewels P., 2016
• Nextflow, Tommaso et al., 2017
• Parallel, O. Tange, 2011
• Prodigal, Hyatt D. et al., 2010
• Prokka, T. Seemann, 2014
• Quast, A. Gurevich et al., 2013
• R-base, R Development Core Team, 2008
  • ggplot2, H. Wickham, 2009
  • ggtree, G. Yu et al., 2016
  • knitr, Y. Xie, 2015
  • plotly, C. Sievert et al., 2017
  • RColorBrewer, E. Neuwirth and R.C. Brewer, 2014
  • reshape2, H. Wickham, 2007
  • rmarkdown, J.J. Allaire, 2015
  • treeio, L-G. Wang et al., 2019
• Roary, A.J. Page et al., 2015
• Samclip, T. Seemann
• Samtools, Li H. et al., 2009
• Shovill, T. Seemann, 2020
• Snippy, T. Seemann
• SnpEff, Cingolani P. et al., 2012
• Tormes, Quijada NM. et al., 2019
• Trimmomatic, A.M. Bolger et al., 2014
• Unicycler, Wick RR. et al., 2017
• Vt, VT

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